Santos striker Neymar, playing only one day after scoring twice for Brazil against Japan in Poland, shrugged off jet leg to score a stunning into the penalty area, cut inside another defender and fired a low shot into the corner of the goal to put his side 2-0 ahead.
Neymar only arrived in Brazil on the morning of the game after the 20-hour trip from Wroclaw where he faced Japan in a friendly.
He has missed several Santos games this season due to Brazil call-ups, including the Olympic Games in London, much to the regret of coach Muricy Ramalho.
"Unfortunately, he has not played much for us this year and has been greatly missed," said Ramalho, whose side are ninth with 42 points from 31 games.
Argentine striker Ezequiel Miralles had put Santos ahead after only 20 seconds, but Atletico Mineiro hit back with goals from Bernard and former Manchester City forward Jo before the half hour.
The game lost momentum after play was halted for 10 minutes following an ugly clash of heads between Mineiro pair Rafael Marques and Leonardo Silva.
Players removed advertising hoardings to try and help the ambulance drive onto the pitch, but it could not get through and Marques had to be taken on a stretcher to the vehicle.
He was taken to a hospital but Atletico said he was not seriously hurt.
Bernard also had to leave the pitch in the second half after another clash of heads but did not need hospital treatment.
Mineiro stayed second in the table, nine points behind leaders Fluminense, who drew 2-2 at home to third-placed Gremio despite Moreno's quick dismissal.
The Bolivian international, who played for his country the previous day in a 4-1 World Cup qualifying win over Uruguay, entered with Gremio 2-1 down and was shown a red card for elbowing Rafael Sobis in the 64th minute.
Former Brazil and Real Madrid coach Vanderlei Luxemburgo's side still managed to snatch a point with a 85th minute goal by Ze Roberto.
Photograph: Lintao Zhang/Getty Images