Rio de Janeiro-based 'Flu' had midfielder Bob sent off just past the hour for a second booking after scoring early goals through fullback Mariano and striker Emerson.
A late goal to Gremio's Andre Lima was not enough to save Silas, who became the 22nd coaching change of the season among the 20 top-flight clubs after only seven months at the helm.
"I'd like to clear up a lie that prejudiced today's outcome saying I'd already said goodbye to the players," Silas told reporters.
"Sao Paulo have not invited me to go there. Whoever has worked with me these last seven months knows the sort of person I am."
The win maintained Fluminense's one-point lead in the championship over Corinthians, whose 1-0 win over title holders Flamengo kept them in a winning vein since coach Mano Menezes left them to take charge of the national team.
Third-placed Ceara have 21 points and Internacional 20 with a game in hand as their match with Santos was postponed to prepare for Wednesday's first leg of the Libertadores Cup final against Guadalajara in Mexico.
"The criticism goes in one ear and out the other," Scolari, back in Brazil after a seven-year absence, said. "The team are playing relatively well, but haven't been lucky, missing chances that should have gone in."
