Unbeaten Atletico Mineiro opened a three-point lead at the top with 17 points from seven matches after a controversial finish to their 3-2 win at Santos.
Adriano, who left Inter Milan in April because he was unhappy in Italy and appeared to have lost his desire for football, opened the scoring the 13th minute when he lobbed keeper Lauro from the edge of the box.
Emerson increased Flamengo's lead in the 36th minute and Adriano, left out of Brazil's Confederations Cup squad due to his recent lack of regular football and form, scored with a left-footed free kick before halftime.
Adriano, who took his tally to four goals in four games, completed a hat-trick with a 68th-minute penalty after defender Leonardo Moura was brought down and despite demands from team mates Ibson and Juan that one of them should take the spot kick.
Flamengo coach Cuca will have been relieved to see his team win at home after 4-2 and 5-0 away defeats in their previous two matches had fans calling for his head.
No such luck for title holders and three-time champions Sao Paulo, who have had a week to forget, having been knocked out of the Libertadores Cup on Thursday by fellow Brazilians Cruzeiro and sacked coach Muricy Ramalho on Friday.
Midfielder Cristian, captain Chico and substitute Juciclei scored for Corinthians, while Ronaldo had a quiet game.
Richarlyson scored for Sao Paulo, who will officially unveil former Brazil captain and Monaco coach Ricardo Gomes as their new trainer on Tuesday and are 16th after one win in seven matches.
At Santos, referee Djalma Beltrame announced four minutes' stoppage time then whistled for the end of the match after only two.
Pressured by the home team's players, he restarted the match to play the remaining two minutes.
Molina then scored what appeared to be a valid equaliser only for the referee to whistle for a dubious foul on another player and send off left back Leo for protesting.
"He (the referee) got scared of complications having made a mistake by ending the game early. So, when he saw the ball go in, he invented a foul. It's absurd," Leo told reporters.
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