Trubisky, who is inactive Thursday, woke up with soreness and had less movement in his injured right shoulder than the team expected Wednesday morning, a source told ESPN's Adam Schefter.
Trubisky has an AC sprain in his throwing shoulder and not a labrum issue, a source told Schefter.
Trubisky, 24, needs rest, and the Bears think he could have played if the game was on Sunday instead of Thursday. The Bears believe that he'll be ready to play in Week 13 against the Giants.
The Bears activated quarterback Tyler Bray to back up Daniel. Earlier in the week, Bears coach Matt Nagy said he was "cautiously optimistic" that Trubisky would play.
Trubisky injured his shoulder on a late hit by Minnesota safety Harrison Smith near the end of the fourth quarter in Sunday night's 25-20 victory over the Vikings.
Chicago will become the first team since the 1970 merger to play a Thursday day game following a Sunday night game, which further complicates Trubisky's predicament.
During Chicago's past six games, Trubisky has 2,832 yards of total offense and has accounted for 23 touchdowns and three two-point conversions. Trubisky had arguably one of the best games of his young career against the Lions on Nov. 11, when he completed 23 of 30 pass attempts for 355 yards, three touchdowns, zero interceptions and one rushing touchdown.
Daniel, 32, hasn't started an NFL game since the 2014 season.
Information from ESPN's Jeff Dickerson was used in this report.