Some 20,000 people in the Olympic Stadium cheered as each of the players, dressed in the red wine coloured "Vinotinto" national strip, was welcomed on stage.
But for a short period before the event began, much of the crowd shouted a popular anti-government slogan, with the chants surging again several times during the ceremony.
"It's going to fall, it's going to fall, this government is going to fall!" the fans sang at the stadium in Caracas.
At one point, the chants became so loud that team coach Rafael Dudamel pleaded with the crowd to quieten down, saying from the stage: "Nobody should steal this moment from us."
Protesters demanding elections, along with an end to food and medicine shortages, have stormed the streets of Caracas and other cities almost every day since early April.
At least 68 people have died in the often violent demonstrations, including protesters, government supporters, bystanders and members of the security forces.
The president says his foes are seeking a violent coup.
Unusually for such an event, Tuesday's homage was not broadcast live on the main state television channel, which instead showed Maduro at an event with army officials. Earlier the team's arrival at the airport was broadcast.
The youth side unexpectedly reached the Under-20 World Cup final in South Korea, the strongest ever performance for a soccer side from a country where baseball has long been the national sport.
Although beaten by England in the final, the players' success has created a rare moment of joint pride amid the bitter political divide and violence.
"Even though they lost, they are our champions. This is the greatest achievement in our football history and we will not forget," said architecture student Roberto Hernandez, 22.
"This country needs some happiness and these kids gave us spadefuls of that every time they won a game."
Though coach Dudamel was judicious in his words on Tuesday, he irked the government last week when, after a semi-final victory, he called on Maduro to "stop the weapons" and lamented the death of a 17-year-old protester.
The violence was unabated on Tuesday, with a 45-year-old police officer shot dead during a demonstration in the mountain state of Merida. State governor Alexis Ramirez condemned the death as an act of "hooded terrorists" who shot at police, injuring two more plus two students.
(Writing by Frank Jack Daniel; Editing by Andrew Cawthorne and Andrew Hay)
