Leaders Fluminense fell behind to a first-minute goal by striker Luan but scored twice in the last 10 minutes to earn the win and stay nine points ahead of Atletico Mineiro, who beat Sport Recife 2-1 at home.
Captain Fred equalised for 'Flu' with a penalty harshly awarded for what looked like an unintentional handball by Luan.
With Ponte Preta down to 10 men after midfielder Wendel's dismissal for a second booking in the 83rd minute, central defender Gum headed the 89th-minute winner from Wagner's free-kick, awarded amid protests from Ponte Preta.
The free-kick was given for a foul on Marcos Junior but television replays appeared to show the decision should have gone the other way with the Flu player the culprit, pulling his opponent's shirt before going down.
Angry fans invaded the club headquarters during the week to protest against the directors, painting slogans on the walls, and travelling supporters also held a demonstration outside the team's hotel in Recife before the match against Nautico.
If Palmeiras are relegated, they will play in Brazil's second division in 2013 while competing for the Libertadores Cup, South America's elite club trophy.
