The defender was a doubt for the fixture against the Giallorossi and was expected to be rested for the game after picking up a knock during last week's 2-2 draw with Juventus in the Coppa Italia; a result which saw Massimiliano Allegri's men crash out 4-3 on aggregate.
However, the former Fluminense defender was put through his own personal warm-up prior to kick-off and deemed fit enough to start versus Roma, only to be hauled off after just 10 minutes with a troublesome flexor muscle.
"Thiago Silva has a problem with a flexor muscle and cannot play in the Champions League against Barcelona. I risked him, but it did not pay off," Allegri told Sky Sport Italia after the match.
Silva's injury could prove to be a big blow for the reigning Italian champions, who are already set to be without a host of players for Wednesday's first-leg encounter against Barca.
Nevertheless, the win against Roma means Milan move seven points clear of Juventus at the summit of Serie A, thanks to a pair of goals from Zlatan Ibrahimovic.