Internacional had defender Indio sent off one minute before half-time and right back Bolivar for a second booking in the final minutes of the match.
They went ahead in the 34th with a header by centre back Fabiano Eller from Argentine playmaker Andres D'Alessandro's corner and added a second 10 minutes from time through midfielder Magrao.
Palmeiras stayed top after a 2-1 win over Barueri on Saturday with striker Vagner Love converting a penalty in his first match since returning to the club on loan from CSKA Moscow until July 2010.
After 23 matches, Palmeiras have 44 points, Inter 43, title holders Sao Paulo 40 and Goias 39 in the four Libertadores Cup qualifying places.
"To be champions we have to win at home and also away which is what we did today...despite the sendings off," Inter forward Tyson told reporters.
Palmeiras went ahead five minutes after the break with a header by midfielder Diego Souza after a long ball from playmaker Cleiton Xavier.
Love, his hair dyed green, increased their lead from the spot after Palmeiras were awarded a penalty when fellow striker Obina ran into a defender in the 73rd minute.
Leandro Castan pulled one back.
Champions Sao Paulo came from behind to beat Libertadores Cup runners up Cruzeiro 2-1 away thanks to goals from substitutes Marlos and Borges.
Marlos, who came on just past the hour, had only been on the pitch three minutes when he equalised with a shot across goal that beat keeper Fabio.
Borges scored the winner from Dagoberto's cross ion the 81st minute, one minute after coming on for Washington.
"It was a match to show we are not out (of the running)," Sao Paulo captain and former Brazil goalkeeper Rogerio Ceni said. "Four points behind, we are still alive."
Last year's Libertadores Cup runners-up Fluminense were held 1-1 by Nautico at the Maracana in their first match under Cuca, their fifth coach of the year, and remain in bottom place.
