The Brazilian, who came on as a substitute in the midweek League Cup semi-final second leg at Swansea City, ended the match limping and is also a doubt for Wednesday's Premier League game at Reading.
"He had a problem before. He had treatment, didn't play the other game (Sunday's 2-1 victory over Arsenal) and we were protecting him," manager Rafael Benitez told a news conference on Friday.
"I was talking with medical staff and him before the (Swansea) game about whether we could take the risk. I waited until the end and didn't want to risk him but we had to play him and after 10 or 15 minutes he felt something and we had to move him to the middle of the park."
Chelsea will also be without midfielder Eden Hazard against Brentford following his red card against Swansea.
The Belgian international received an automatic three-match ban for kicking a ballboy who was stopping him from retrieving the ball but could face a longer suspension after the FA charged him with violent conduct on Friday.
Chelsea are hoping to avoid a second cup exit in a week after losing 2-0 on aggregate to Swansea but they know third tier Brentford are sure to be fired up for the west London derby.
"It will be a tough game, it's a massive game for them and they will be pushing, playing between long and short passes and then trying to win second balls. They're an interesting team and doing well," Benitez said.
"We play away and it's a cup competition. It will be different and our approach has to be different. The pitch is not the best, totally different, but it's a game we play against a nearby team which will be a massive motivation for them too."