The assumption was wrong.
While Smith's concussion did not prevent him from practicing during the week, it will prevent him from playing against the Chicago Bears, ESPN's Chris Mortensen reports. According to Mortensen, Smith was "unable to get clearance from a neurologist" to play in the game.
That means second-year pro Colin Kaepernick will make his first NFL regular-season start against arguably the best defense in the league. The Bears will be without their starting quarterback, Jay Cutler, also because of a concussion. Their backup, Jason Campbell, owns 70 regular-season starts and a 31-39 record in those games.
Kaepernick played effectively during the latter stages of the 49ers' 24-24 tie against St. Louis in Week 10. He completed 8 of 9 passes and rushed for four first downs with a touchdown during the fourth quarter and overtime of that game. He took three sacks and fumbled twice overall, however. He was off-target with some throws while completing 3 of 8 passes immediately upon replacing the concussed Smith in the second quarter.
Reports have suggested Smith took all the meaningful practice reps in anticipation of playing against the Bears. If that is the case, the 49ers would appear to be at a quarterback disadvantage going into the game. Even so, the staff had to know there was a chance Kaepernick would play. The game plan will presumably take advantage of his strengths as a runner and of his strong arm.