James Daniels and Bobby Massie were whistled for penalties in the first half, and Charles Leno was called for holding on the Trubisky scramble that resulted in a late hit and sideline kerfuffle.
The game turned feisty in the fourth quarter, when San Francisco safety Marcell Harris hit Trubisky after he started sliding on a scramble near the Bears bench.
"Even though we have the playoffs locked up already, we want to finish strong and that's our mindset", quarterback Mitchell Trubisky said.
The 49ers finally got a takeaway. "We know what kind of player [Robinson] is, and he rarely makes mistakes like that". But CB Tarvarius Moore punched the all out from behind and the Niners had the ball down 14-9 with 1:52 remaining. You're going to do all that, you let him go. Miller said. "And I don't support that".
Allen Robinson made a number of critical catches, and five of his eight receptions went for a first down - though that includes the last one he caught, which he fumbled after crossing the line to gain.
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The Bears have allowed a total of one touchdown in the past three games.
Former Bears kicker Robbie Gould kicked three field goals in the first half against his former team after making all five in a 15-14 win at Chicago a year ago.
I just think everyone would feel a whole lot better about the Bears' chances if the team that pounded the Rams and Packers had shown up in San Francisco.
With Jackson out, S Deon Bush will get his first start of the season.
Rookie DL Bilal Nichols (knee), who was limited on Friday as a precautionary measure, is active.
The Bears' other inactives were receivers Kevin White and Javon Wims, quarterback Tyler Bray, offensive lineman Rashaad Coward and defensive lineman Nick Williams.