The 49ers scored a season-low three points and gained only 164 yards on offense, their lowest total since a 10-9 loss to the Panthers last November. Quarterback Colin Kaepernick completed 16 of 29 passes for 121 yards and threw two interceptions.
The San Francisco offense gained 3.2 yards per play, while its defense allowed 6.3 yards per play.
York and coach Jim Harbaugh have long been reported to be at odds with one another, though York refuted a report in October which said there was "no way" Harbaugh returned in 2015.
- Dan Gartland