49ers running back Raheem Mostert hobbled off to take a seat on the bench in the third quarter. He is rubbing his left ankle in obvious pain.
His day could be over after 14 carries for 68 yards. The 49ers list him as questionable to return.
The 49ers already have ruled out defensive end Dion Jordan (knee) and safety Jimmie Ward (concussion).
But Robbie Gould has made a 41-yard field goal with 10:48 remaining in the third quarter to tie the Cowboys 17-17.
Nick Mullens is 11-of-18 for 120 yards and two touchdowns. Richie James has three catches for 49 yards.
Mullens and James both lost fumbles, helping the Cowboys take an early 14-0 lead.