The Dodgers had taken a 3-0 lead in the first on James Loney's three-run homer off Silva. In the second, Los Angeles loaded the bases and Matt Kemp hit a sacrifice fly. Andre Ethier was intentionally walked and Loney then hit a grounder toward Xavier Nady at first.
Nady picked up the ball and appeared to beat Loney to the bag, but first-base umpire Brian Runge called Loney safe.
Silva had run over to first and threw up his arms in disgust at the call. Runge then tossed him.
The Cubs right-hander was questionable for Sunday's game because of some discomfort in his right calf.
On Saturday, umpire Jerry Layne ejected manager Lou Piniella after he argued a close play at first base that replays also appeared to support the Cubs manager. Layne was behind home plate on Sunday.