The meeting had had been expected to bring together the leaders of the eight nations that have territory inside the huge rainforest region.
But in the end the only leaders to attend were Lula, Guyana's president, Bharrat Jagdeo, and Nicolas Sarkozy, the French president, representing the overseas territory of French Guiana.
Al Jazeera's Gabriel Elizondo, reporting from Manaus, said the meeting had been thrown together at the last minute.
Having failed to reach a common agenda, he said, the Amazon countries will now head to Copenhagen with divergent approaches – threatening to slow progress at a meeting that is already suffering from setbacks and lowered expectations.
"They apparently got some confirmation over the last few days that the heads of state would be coming, but then at the last minute several of them pulled out," he said.
"This is definitely a very embarrassing issue for Lula."
Relations between the leaders of Venezuela and Colombia are poor due to a dispute over Bogota's agreement to allow US forces greater access to military bases in the country.
A series of border incidents, including the destruction of two footbridges by Venezuela, have led Colombia to last week to put its forces on "maximum alert".
"There has been a lot of sabre-rattling been going on between those two countries," our correspondent said.
"So I think once Hugo Chavez said he wasn't going to come, then Uribe decided he was going to go either. I think there was a bit of political one-upmanship."
Environmental activists gathered in Manaus before the talks to urge leadership at the climate summit in Copenhagen.
"We are sending a message to Obama, Lula and Sarkozy. Actually, it is for all world leaders. There is no more time for talks," Paulo Adario, Greenpeace's Amazon co-ordinator, said.
"Either they take on a historic role to fight and make something concrete in Copenhagen and go down in history or they will go to waste."