The 39-year-old keeper, who has scored more than 100 goals in his career from penalties and free-kicks, had been out of action since last November with a shoulder injury.
Former Brazil striker Luis Fabiano scored two of the goals for Sao Paulo, who gave Flamengo's new coach Dorival Junior plenty of food for thought in only his second game in charge.
Palmeiras dropped into the relegation zone with a 2-1 defeat at Cruzeiro which ended with their players surrounding the referee furiously protesting his decisions.
The referee left the pitch with a police escort as the Palmeiras team remonstrated over the penalty award which led to Borges giving Cruzeiro the lead before half-time. They were also livid over a disallowed goal.
Palmeiras coach Luiz Felipe Scolari, who led Brazil to their World Cup victory in 2002, refused to talk to the media after the match.
Borges also scored Cruzeiro's second goal with Hernan Barcos pulling one back for Palmeiras, who are 18th in the 20-team table with 10 points from 13 games. The bottom four go down.
Atletico Mineiro stayed top with a goalless draw at Fluminense. They are two points clear of Vasco da Gama, who were also involved in a 0-0 draw with Internacional.