Criciuma's Souza cancelled out Edson Silva's opener at the Heriberto Hulse stadium before Alan Kardec headed in the winner seven minutes from time.
Sao Paulo remain second in the standings, five points behind Cruzeiro with six matches remaining.
Meanwhile Flamengo rose to 10th with a 3-0 victory over Chapecoense at Rio de Janeiro's Maracana stadium.
Midfielder Nixon struck twice while Anderson Pico was also on target for the hosts.
In Belo Horizonte, first-half goals from Marquinhos and Egidio gave Cruzeiro a 2-1 victory over Botafogo. Leo gifted the Rio outfit a consolation goal by turning the ball into his own net in second-half injury time.
In other matches on Sunday, Santos lost 2-1 at home to Internacional, Sport defeated Goias 1-0 Adidas Yeezy Boost 350 V2 Black Red UK , Atletico Paranense beat Atletico Mineiro 1-0 and Palmeiras won 1-0 at Bahia.