Linebacker NaVorro Bowman sustained an apparent left foot injury in the third quarter that forced him out of the game.
Bowman walked slowly to the 49ers' bench after a play on which Dallas quarterback Dak Prescott threw an 11-yard pass to Brice Butler. Bowman was not involved in the play.
The team's medical staff removed Bowman's left shoe and examined his foot, heal and Achilles areas.
Bowman was taken back into the locker room on a cart for further observations. The team announced that Bowman would not return due to a "lower leg" injury.
Nick Bellore, who replaced Bowman, joined Michael Wilhoite as the 49ers' inside linebackers. Wilhoite started in place of Gerald Hodges.
The Cowboys ended up driving on the 49ers to score on Ezekiel Elliott's 1-yard touchdown run for a 21-17 lead over the 49ers.
The injury does not appear related to the left knee injury Bowman sustained in January 2014 in the NFC Championship game. Bowman did not play during the 2014 season before returning to action last year.
