The champions paid the price for resting their first team regulars with an eye to Wednesday's semi-final, second leg of the Libertadores Cup at home to holders Santos.
Corinthians, determined to win the continental crown for the first time, are bottom of the domestic championship standings with one point from five matches.
None of the eleven players who started last Wednesday's upset 1-0 win at Santos in the first leg of the Libertadores semi-final took part in the match against Ponte Preta at Campinas deep in Sao Paulo state.
Striker Andre Luis scored the only goal with a header three minutes before halftime.
Santos are only slightly better off in the championship with three points from three draws as they also keep their best players fresh for their bid to win the Libertadores for the fourth time.
They lost 1-0 to Flamengo at the Engenhao in Rio de Janeiro. Argentine substitute midfielder Dario Bottinelli scored the winner with a penalty two minutes from time.
Vasco da Gama, eliminated by Corinthians in the Libertadores quarter-finals in mid-May, stayed top and unbeaten with 13 points after a 1-1 draw away to Palmeiras.
Former Olympique Lyon and Brazil midfielder Juninho secured the point when he equalized with a trademark free kick eight minutes from the end.
Ronaldinho's new club Atletico Mineiro lost their unbeaten record when they went down 1-0 at Sao Paulo.
Former Brazil striker Luis Fabiano scored in the 41st minute before being sent off five minutes from the end of the match when he was booked for dissent, his second yellow card.
Mineiro are third with 10 points, one less than their arch-rivals Cruzeiro from the city of Belo Horizonte.