Atletico were the better team throughout the match but needed a headed goal by central defender Leonardo Silva from Ronaldinho's cross three minutes into added time to secure the three points.
Fluminense had their lead cut to six points with six matches remaining as they chase a second Brazilian title in three seasons.
"We cut the points difference and now we can believe more in [winning] this title," former FIFA world player of the year Ronaldinho told reporters.
"We came to this match against direct [title] rivals with a certain margin and could afford to lose a bit of it today," Fluminense's goalkeeper Diego Cavalieri said.
The teams were level at half-time only because Cavalieri made a string of saves to keep "Flu" in the game and two shots hit the posts.
Ronaldinho laid on the equaliser in the 69th minute for Jo, who shot high into the net, and the striker headed Atletico in front 13 minutes later from young midfielder Bernard's cross.
Flu captain Fred equalised four minutes from time but Leonardo's winner from Ronaldinho's perfect cross dashed his team's hopes of keeping their nine-point lead.
