Sao Paulo, who had won their first five matches, conceded all the goals in the second half after defender Carlinhos Paraiba was sent off just minutes before half-time for a second booking.
It was their worst ever defeat against their arch-rivals in Brazilian championship matches and narrowed their lead in the standings to two points over Corinthians, who have a game in hand.
"This brought us back down to earth. It was a good lesson," Sao Paulo striker Dagoberto told reporters as he left the pitch.
The former FIFA World Player of the Year, blamed for Flamengo's recent indifferent form, hit a superb 67th-minute equaliser into the top corner after midfielder Dudu Cearense had headed the visitors into the lead.
Ronaldinho, booed off after last weekend's 0-0 draw with Botafogo, had his name chanted by the fans. Midfielder Thiago Neves also scored and striker Deivid scored hit a brace in the last five minutes.
