The 40-year old keeper, who made his debut in 1993, takes most of the team's free kicks and penalties and has scored 113 times, more than any other goalkeeper.
However, he could do little to stop his unfancied opponents, playing in their first international competition, from grabbing a crucial first-leg lead.
Paulo Henrique Ganso's 20th minute goal was cancelled out by an own goal from Antonio Carlos seconds before halftime, and then Leonardo slipped home a loose ball after Ceni could only parry a Fernando Bob shot in the 52nd minute.
Uendel added a third 19 minutes later when his deflected shot wrongfooted the Sao Paulo goalkeeper.
The second leg takes place next week with the winner facing Argentine side Lanus or Paraguay's Libertad in the final next month.
Before that, Ceni is expected to overtake Pele's mark when he turns out against Botafogo in the league on Sunday.
Also on Wednesday, Atletico Paranaense drew 1-1 with Flamengo in the first leg of the Brazilian Cup final.
Marcelo opened the scoring for the home side with an unstoppable 25-year drive in the 17th minute but Amaral equalised for Flamengo 12 minutes later with an equally impressive strike from far out.
The return match takes place at the Maracana next Wednesday and Flamengo are confident they will lift the trophy in front of their home fans.
"We lost an early goal but our heads didn't go down and we played well considering we were away from home," said keeper Felipe.
"A lot of our fans came a long way for this game and that inspires us. In front of 80,000 supporters at the Maracana we'll do our best to repay them."