Heisman Trophy candidate Griffin left with an injury after accounting for three touchdowns. He took a shoulder to the head from Texas Tech's Cornelius Douglas on a hit late in the first half that was ruled a personal foul and lay motionless on the field before eventually walking off.
Griffin spent the second half on the sidelines as the Bears (8-3, 5-3 Big 12) won their fourth straight.
Terrance Ganaway rushed for 246 yards and two scores, and Joe Williams returned an interception 90 yards for a touchdown early in the second half for Baylor.
The Red Raiders (5-7, 2-7) lost to the Bears for the first time since 1995.