Television pictures showed police using pepper spray to control fans at the Alligator Arena in Sete Lagoas which is being used as a substitute stadium while Belo Horizonte's Mineirao is rebuilt for the 2014 World Cup.
There was also trouble on Saturday when around 250 Cruzeiro fans gathered in front of the team's training ground to protest the relegation-threatened team's recent results.
Fans surrounded the players' cars as they arrived at the training ground and hurled insults, local media reported.
Souza, voted the championship's top player in 2009 when he was playing for Palmeiras, opened the scoring with a low shot five minutes before halftime and tapped in the second on the hour from full-back Fagner's cross.
He saved the best until last, cleverly flicking the ball over Cruzeiro goalkeeper Fabio before heading into the net in the 81st minute.
Cruzeiro's misery was completed by a red card for defender Marquinhos Parana for a professional foul on Souza.
Vasco lead with 49 points from 26 matches, two ahead of Corinthians who beat Bahia 1-0.
Sao Paulo stayed third with 46 after former Brazil and Barcelona playmaker Rivaldo came off the bench to score an injury-time equaliser in a 2-2 draw at Botafogo, who are fourth.
The 39-year-old, who returned to Brazil last year after a three-year spell in Uzbekistan, headed in a free-kick taken by goalkeeper Rogerio Ceni two minutes into stoppage-time.
