Three times South American champions Sao Paulo, who were without suspended forwards Luis Fabiano and Jadson for the Group Three decider at the Morumbi, will clash again with tournament favourites Atletico in the first knockout round.
Ceni, who has scored more than 100 goals from free kicks and penalties, converted from the spot with a well-placed shot into opposite number Victor's top left-hand corner after Aloisio brought down Leonardo Silva early in the second half.
The Sao Paulo captain had spent more than a week nursing a sore right foot and said if he had to take a penalty it could only be to that side, where he also scored from the spot against Bolivia's The Strongest in a 2-1 defeat in La Paz two weeks ago.
Ceni praised Brazil midfielder Paulo Henrique Ganso, interrupting an interview on television to say to him: "You were the best of the match. Now I understand why you are worth what you are."
Ganso, one of the most creative midfielders in Brazil who eclipsed Atletico's Ronaldinho on Wednesday, has struggled to find his best form since joining Sao Paulo from Santos last year.
He warned Atletico that his side would be stronger in the two-legged last-16 clash, saying: "It will be a different Sao Paulo, even better and with much more will than today."
Sao Paulo, boosted by their passionate crowd of 50,000, sealed victory with a second goal from teenager Ademilson nine minutes from time but needed help from Argentina's Arsenal to advance.
The Strongest were second in the group before Wednesday's deciding round of matches and a win in Buenos Aires would have put them through with Atletico, the only team in the competition with a perfect record of five wins.
Arsenal, who also stood a chance of qualifying if Sao Paulo did not win, beat the Bolivian champions 2-1 to finish third behind the Brazilian side on goal difference.
The only matter at stake in the final round of matches in Group One was first and second place and there was no change as the two teams that had qualified both lost.
Nacional of Uruguay, three times trophy winners, lost 1-0 away to Ecuador's Barcelona in Guayaquil but stayed top as second-placed six-times champions Boca Juniors also lost 3-2 at Toluca in Mexico.
Struggling Boca, who languish near the bottom of the Argentine 'Final' championship with eight points from nine games, lost for the sixth time in 15 matches this year and will need a dramatic improvement to reach a second consecutive Libertadores Cup final.
- Sports & Recreation
- Sao Paulo
- Paulo Henrique Ganso