Smith was hit hard by Rams linebacker Jo-Lonn Dunbar on a 4-yard run in the first quarter. He remained in the game long enough to connect with receiver Michael Crabtree on a 14-yard touchdown pass, but was in obvious discomfort on the sideline before leaving for the locker room with his helmet off. Smith finished 7 of 8 passing with 72 yards and the score.
Colin Kaepernick took over on the following drive. Coach Jim Harbaugh told FOX at halftime he believed in his backup, but if San Francisco hoped to take a wider look at Kaepernick under center, this isn't the way the team wanted it to happen. Smith is a popular target for critics, but he's become one of the of the NFL's highest-rated passers in Harbaugh's ground-heavy system.
Kaepernick has made operating the Wildcat look easy this season, but running the entire show is a different story.
Follow Marc Sessler on Twitter @MarcSesslerNFL.