Menezes, who takes over as Brazil coach on Monday when he is due to name a squad for a friendly away to the United States next month, was given a standing ovation by the supporters.
"I'm leaving on a high," he told reporters after his last game as Corinthians coach on Sunday. "I think the coach has played a part in everything Corinthians have achieved since we started here at the start of 2008."
Menezes, who led Corinthians out of the second division in his first season in charge in 2008, will be replaced by Adilson Batista, who was fired by Cruzeiro last month.
Corinthians playmaker Bruno Cesar scored twice in the last 10 minutes to give his side the points with both teams already having had a man sent off.
Corinthians, who have 24 points from 11 games, overtook Fluminense, whose coach Muricy Ramalho was offered the Brazil job before Menezes on Friday but turned it down after his club refused to release him.
Fluminense were held 1-1 by Botafogo in a bad-tempered derby which produced three red cards - Fluminense substitute Thiaguinho was dismissed four minutes for time for retaliation while Botafogo pair Somalia and Danny Morais followed in quick succession for second yellow cards.
Third-placed Ceara, three points behind Fluminense, were held to a goalless draw by Luiz Felipe Scolari's Palmeiras.
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