Morales, long a fierce critic of U.S. policy toward Latin America, received a hero's welcome in an airport in the Bolivian capital of La Paz late Wednesday night. His return followed the dramatic, unplanned 14-hour layover in Vienna.
Bolivia's government said France, Spain and Portugal refused to let the president's plane through their airspace because of suspicions that Snowden was with Morales.
Ahead of the meeting, Morales had said that his ordeal was part of a plot by the U.S. to intimidate him and other Latin American leaders.
He urged European nations to "free themselves" from the United States. "The United States is using its agent (Snowden) and the president (of Bolivia) to intimidate the whole region," he said.
France sent an apology to the Bolivian government. But Morales said "apologies are not enough because the stance is that international treaties must be respected."
Spain's Foreign Affairs Minister Jose Manuel Garcia-Margallo said his country did not bar Morales from landing in its territory.
Amid the tensions, the U.S. embassy in La Paz cancelled Independence Day celebrations scheduled for Thursday. In the eastern city of Santa Cruz, Bolivian government sympathizers painted protest slogans on the doors of the American consulate.
Morales said he never saw Snowden when he was in Russia, and that Bolivia had not received a formal request for asylum for him.
Bolivia has said that it will summon the French and Italian ambassadors and the Portuguese consul to demand explanations.
Despite the complaints, there were no signs that Latin America leaders were moving to bring Snowden to the region that had been seen as the most likely to grant him asylum.
All of the region's leaders are not expected at the summit.
Brazil was represented at the meeting by Marco Aurelio Garcia, President Dilma Rousseff's top international adviser. He traveled to Cochabamba with government officials, although Foreign Minister Antonio Patriota missed the summit because he is currently attending meetings in Europe.
The presidents of Colombia, Chile and Peru, who have strong ties to the U.S., were not attending.
Colombian President Juan Manuel Santos said earlier on Thursday that he supports Morales, but asked other leaders to remain cool and avoid an escalating dispute between Latin America and the European Union.
"We're in solidarity with Evo Morales because what they did to him is unheard-of, but let's not let this turn into a diplomatic crisis for Latin America and the EU," Santos wrote Thursday on Twitter.
It's still unclear whether European countries did block the plane and, if so, why. French, Spanish and Portuguese officials have all said the plane was allowed to cross their territory.
The emergency stop in Austria may have been caused by a row over where the plane could refuel and whether European authorities could inspect it for signs of Snowden.
The U.S. has declined to comment on whether it was involved in any decision to close European airspace, saying only that "US officials have been in touch with a broad range of countries over the course of the last 10 days," about the Snowden case.