The victory ended Fluminense's run of five games without a win and also halted Gremio's nine-match unbeaten run at their Enganhao ground.
Captain Conca put his side ahead in the 20th minute with a long shot that flew into the top corner of Brazil goalkeeper Victor's net and added the second after exchanging passes with striker Washington.
"It's going to be tough to break away (from the rest) because the teams are all very even but it was a great victory against a side with some outstanding players," Flu coach Muricy Ramalho told reporters.
"(Conca) made the difference, he scored the goals, organised the team, played the ball. He joined Washington (in attack) so as not to leave him isolated up front. He had a very good game tactically."
With six games remaining, Flu have 57 points, three more than Corinthians, held 1-1 by champions Flamengo on Wednesday, and Cruzeiro, who face bottom side Prudente on Saturday.
Former Brazil striker Ronaldo scored only his third goal of the championship on Wednesday to put Corinthians in front but Diogo headed a second-half equaliser.
Injury-hit and overweight, Ronaldo's latest appearance meant he played three matches in a row for the first time in the championship.
