Latin American leaders immediately called for an emergency meeting of the Union of South American Nations, which was expected to take place on Thursday. Cristina Fernández de Kirchner, the president of Argentina, said the episode had "vestiges of a colonialism that we thought was completely overcome," adding that it was a humiliating act that affected all of South America. President Rafael Correa of Ecuador said in a post on Twitter that the situation was "EXTREMELY serious" and called it an "affront to all America," referring to Latin America.
The diplomatic skirmish began with a seemingly offhand remark. Mr. Morales was flying home on Tuesday from Moscow, where he had attended a meeting of natural-gas exporting nations, and had told Russian television that he was open to giving asylum to Mr. Snowden.
Mr. Snowden has been holed up at Sheremetyevo Airport in Moscow for more than a week, hoping to receive a positive response to the asylum requests he has made to several countries, and Mr. Morales's remark may have set off suspicion that he was bringing the fugitive aboard.
After taking off from Moscow, Mr. Morales's plane asked permission to land in France to refuel, according to Carlos Romero, the minister of government in La Paz. But France refused and denied the plane permission to enter French airspace, Bolivian officials said. Portugal had also previously refused to let the plane land for refueling in Lisbon.
Mr. Morales was finally given permission to land in Vienna, where he spent the night. Mr. Morales told reporters in Vienna that he had not met Mr. Snowden in Moscow and that he had previously known little about the case.
Karl-Heinz Grundböck, a spokesman for the Austrian Interior Ministry, said that the Austrian border authorities carried out a routine check of the passports of everyone aboard Mr. Morales's plane after it landed and that they were also granted permission to search the plane to ensure that Mr. Snowden was not aboard. "The rumors were just that," Mr. Grundböck said.
But in La Paz, officials said that no search had taken place, asserting that it would be improper to search the plane of a head of state. As for the forced diversion of the flight, the vice president of Bolivia, Álvaro García Linera, equated it to a kidnapping.
"Yesterday was one of the most shameful pages in the political history of some countries in Europe," Mr. García Linera said in La Paz on Wednesday.
For many in the region, the episode was a throwback to the colonial era, when European countries held sway over a weak Latin America. Many also blamed the United States, insisting that the Obama administration had instructed its European allies to stop Mr. Morales's plane on the suspicion that it carried Mr. Snowden, who is wanted on charges of violating espionage laws for divulging secrets about American surveillance programs.
After European nations cleared Mr. Morales to fly, he took off from the Vienna airport at about 11:30 a.m. local time on Wednesday and later stopped for refueling in the Canary Islands, which belong to Spain. He was expected to make another refueling stop in Brazil before arriving home in La Paz on Wednesday night.
Austria's president, Heinz Fischer, told state radio that he visited Mr. Morales before his departure to "ensure that our procedures here in Vienna were all correct." The two leaders also had the opportunity to discuss other topics, Mr. Fischer said, but declined to elaborate.
Mr. Morales appeared Wednesday morning before reporters who had gathered at the airport as rumors spread that Mr. Snowden might be aboard, ORF, an Austrian public television network, reported.
"At the moment there is nothing we can do but wait for permission for a flyover," said Mr. Morales, speaking through a translator. "Spain is now consulting with the U.S.A. whether the plane can fly over Spanish airspace." The president, his staff and four pilots were forced to spend the night in the airport's V.I.P. area. Mr. Morales referred to his unscheduled stop in Vienna as "being held hostage."
Asked by a reporter about Mr. Snowden's presence on his airplane, Mr. Morales declined to comment directly, but insisted that it would be impossible to take along a passenger who no longer holds a valid passport. The United States revoked Mr. Snowden's passport on June 22 after charging him with espionage.
"How could we have a person in our plane who has problems with his homeland? He has never sought asylum in Bolivia," Mr. Morales said. "We are very responsible in our actions and our respect for international conventions."
After the plane touched down in Vienna, the foreign minister of Bolivia, David Choquehuanca, said of the refusal by some European countries to allow the president's plane in their airspace: "They say it was due to technical issues, but after getting explanations from some authorities we found that there appeared to be some unfounded suspicions that Mr. Snowden was on the plane."
"We don't know who invented this big lie," Mr. Choquehuanca said at a news conference in La Paz. "We want to express our displeasure because this has put the president's life at risk."
Before Mr. Morales's plane left the Vienna airport, the crew awaited authorization to continue through other European countries' airspace, the Austrian authorities said. France granted authorization Wednesday morning, although a spokesman for the Spanish Foreign Ministry said it would not comment, and there was no immediate comment from Portugal.
Rubén Saavedra, the Bolivian defense minister, who was on the plane with Mr. Morales, accused the Obama administration of being behind the action by France and Portugal, calling it "an attitude of sabotage and a plot by the government of the United States."
There was no immediate response by officials in Washington.
"We were in flight; it was completely unexpected," Mr. Saavedra said on the Telesur cable network. "The president was very angry."
In a possible sign of further suspicion about the passenger manifest, Mr. Saavedra said Italy had also refused to give permission for the plane to fly through its airspace.
On Monday, Mr. Morales, who was attending an energy conference in Moscow, was asked in an interview on the Russia Today television network if he would consider giving asylum to Mr. Snowden.
"Yes, why not?" Mr. Morales responded. "Of course, Bolivia is ready to take in people who denounce — I don't know if this is espionage or monitoring. We are here."
He said, though, that Bolivia had not received a request from Mr. Snowden, despite news reports to the contrary.
It was already clear by then that the Moscow conference had been overshadowed by the drama of Mr. Snowden and his disclosures about American intelligence programs, which have deeply embarrassed the Obama administration.
President Nicolás Maduro of Venezuela, who was also at the conference, suggested that he would offer Mr. Snowden asylum but said he did not plan to fly him to Venezuela.
But Mr. Morales's remarks appeared to open the door. At least that is the way they were interpreted.
The problems began even before Mr. Morales left Moscow, Mr. Choquehuanca said. On Monday, Portugal, without explanation, withdrew permission for Mr. Morales's plane to stop in Lisbon to refuel, the foreign minister said. That required Bolivian officials to get permission from Spain to refuel in the Canary Islands.
The next day, after taking off from Moscow, Mr. Morales's plane was just minutes from entering French airspace, according to Mr. Saavedra, when the French authorities informed the pilot that the plane could not fly over France.
There was also plenty of confusion in Moscow over how Mr. Snowden could possibly have left undetected on a government aircraft.
Government planes carrying foreign officials to diplomatic meetings in Moscow typically arrive and depart from Vnukovo Airport, which is also the main airfield used by the Russian government, rather than from Sheremetyevo, to which Mr. Snowden arrived from Hong Kong on June 23, hours after American officials had sought his extradition.
The speculation that Mr. Snowden would hitch a ride on a government jet was discounted by the fact that the plane would have to first make a quick flight from one Moscow airport to the other.
In an interview with Russia Today, Mr. Maduro said he would consider any request by Mr. Snowden. Then, ending the interview with a dash of humor, he said, "It's time for me to go; Snowden is waiting for me."
William Neuman reported from Caracas, Rick Gladstone from New York, and Melissa Eddy from Berlin. Reporting was contributed by Scott Sayare from Paris, Raphael Minder from Madrid, David M. Herszenhorn and Andrew Roth from Moscow, and Monica Machicao from La Paz, Bolivia.
