South American football's governing body Conmebol had banned the Brazilian club's fans after they let off a flare that killed a 14-year Bolivian supporter during last week's game against San Jose in Bolivia.
Conmebol ordered Corinthians to play their Libertadores games behind closed doors for the next 60 days or until a full appeal can be heard. Their fans are also banned from away matches.
The eerie atmosphere did not seem to bother the holders, who scored in the 10th minute and never looked like relinquishing control of the match.
Peruvian striker Pablo Guerrero opened the scoring when he pounced on a loose ball from a corner and smashed it into the roof of the net.
Alexandre Pato should have extended the lead seven minutes later when he was through with just the goalkeeper to beat but he bundled the ball wide, though the former AC Milan striker made amends at the start of the second half when he side-footed home a cross from Ralf.
Pato and substitutes Emerson and Romarinho all had chances to extend Corinthians' lead but the match petered out and the Brazilian side seemed content with a 2-0 win.
"It was a strange experience," full-back Fabio Santos said.
"We knew we'd need to concentrate and we managed that and not to lose a goal. But I hope that the fans are back for the next game because this was terrible."
The day's real action took place off the field in courts and outside the stadium where Corinthians unsuccessfully tried to overturn the ban, though four fans who won a court appeal were allowed in to watch the game.
A hundred or so fans also gathered outside the ground in the hope their cheers would carry over the elegant art-deco walls of the stadium.
"We mourn for the boy but what can we do," said fan Alexandre Pedro. "We will still be cheering for our team. This club will never be without its fans."
The victory lifted Corinthians, who won the Libertadores last July and the World Club Cup in December, to second place in Group 5 behind Mexican side Tijuana.
The two teams meet in Mexico next week.