There were three men dismissed in Gremio's goalless draw with Internacional too, a result that saw them surrender a one-point advantage to Atletico and slip into third place.
Back at the Estadio Raimundo Sampaio, Bernard had the Atletico rooster crowing after just five minutes but Alejandro Martinuccio equalised deep into first-half stoppage time after Ronaldinho missed a penalty for the hosts in the 38th minute.
Everton nudged the visitors ahead six minutes after the break and soon both teams were in disarray, with Cruzeiro's Tinga and Atletico's Leandro Donizeti picking up red cards in what was a fractious 55th minute.
Marcelo Oliveira's own-goal drew the hosts level on the hour mark before Ronaldinho set up Rever for the winner in the 75th minute. There was still time for Anselmo Ramon to pick up a second yellow card that saw Cruzeiro finish the game with nine men.
There were no goals over at the Estadio Olimpico Monumental in Porto Alegre but Gremio lost substitute Saimon to a red card late on, after Internacional goalkeeper Muriel and striker Leandro Damiao had been dismissed either side of half-time.
It was too late for Vasco de Gama to snatch a Copa Libertadores spot but a 2-1 win at Fluminense earned a creditable fifth-placed finish.
Eder Luis struck twice in the last 20 minute for the visitors, leaving Thiago Carleto to halve the deficit from the penalty spot four minutes from time.
Sao Paolo had already wrapped up fourth place and continental football but there was still time for a 3-1 victory at home to Corinthians.
The visitors were briefly ahead thanks to Paolo Guerrero (13) but Douglas equalised two minutes later and Sao Paolo never looked back.
Maicon scored either side of Jorge Henrique's 68th-minute dismissal, with home striker Willian Jose seeing red in the 90th minute.
Everton Ribeiro ensured a comfortable mid-table finish for Coritiba with two goals in a 3-0 win over basement boys Figueirense, with Denis also on target.
Clemerson Araujo's 65th-minute strike gave Nautico a 1-0 victory at home to Sport Recife - with the hosts missing a late penalty - and 10-man Portuguesa played out a goalless draw with Ponte Preta.
Elsewhere, Bahia finished 15th as a solitary Rafael goal settled a 1-0 victory at relegated Atletico Goianiense.