"I haven't come here to fight. I was pleased to shake hands with the German chancellor," Chavez was quoted as saying at a summit of European and Latin American leaders in the Peruvian capital, Lima.
"I told her that I was sorry if I'd been harsh," he said, according to Peru's state news agency Andina.
Photographs showed the two smiling as they shook hands while heads of state mingled at the gathering dedicated to tackling poverty and climate change.
Merkel, a conservative, had sought to play down the spat before her arrival in Lima, saying she would greet all delegates courteously.
Earlier this week, Chavez made his Hitler comments after Merkel implied the leftist leader had harmed relations between Europe and Latin America.
Chavez routinely insults conservative leaders, especially US President George W. Bush, calling him the devil.
During a summit in Chile late last year, Spain's king told the socialist leader to "shut up."