SANTA CLARA -- Two mistakes could have cost Colin Kaepernick his job. Instead, his response to those two botched plays cemented his status as the 49ers' starting quarterback for Sunday's game against the Miami Dolphins.
Coach Jim Harbaugh confirmed Monday that he was sticking with Kaepernick over Alex Smith, pointing largely to the way his second-year quarterback rebounded from the miscues against the St. Louis Rams.
"There were real positives to take away from his performance," Harbaugh said.
A 16-13 overtime loss Sunday left plenty of room for frustration, including questionable play-calling by the coaching staff (Harbaugh acknowledged as much and accepted the blame) and another missed field goal from David Akers (whose job is also safe, the coach said).
But the most memorable gaffe came on an option-read late in the fourth quarter. With the 49ers clinging to a 10-2 lead, Kaepernick airmailed his toss to receiver Ted Ginn Jr. in the backfield.
The ball sailed over Ginn's head and skittered toward the end zone, where cornerback Janoris Jenkins pounced on it and rolled across the goal line for a gift touchdown that helped the Rams tie the score.
Harbaugh reiterated Monday that the play was the coaching staff's fault, not Kaepernick's. He said he should have vetoed offensive coordinator Greg Roman's play call. On a third-and-3 from the Rams' 17-yard line, this was no time to get fancy.
"Too much ballhandling, too much chance for the play to go sideways and backwards and at that point of the game. I take responsibility for that," said Harbaugh, who said Roman called a strong game overall.
Ugly as the play was, Kaepernick won praise from Harbaugh for settling things down on the next drive. On the first offensive snap after the botched fumble, the quarterback connected with Michael Crabtree for a 16-yard gain. On the second snap, he blazed 50 yards down the right sideline to set up Akers' go-ahead field goal.
"Just a winning quarterback performance in tough circumstances," Harbaugh said.
The coach also pointed to Kaepernick's response in the aftermath of a controversial safety in the third quarter. On a first-and-10 from the 17-yard line, Kaepernick retreated all the way into the end zone before firing the ball out of bounds under defensive pressure.
Officials threw a penalty flag for intentional grounding, crediting the Rams with a safety that cut the 49ers' lead to 7-2.
Still, Harbaugh was encouraged by what happened next: On the 49ers' next possession, which started at the 1-yard line, Kaepernick directed a 13-play, 94-yard drive capped by Akers' field goal.
"He made some big-time plays in that situation and throughout the course of the game," Harbaugh said.
Kaepernick completed 21 of 32 passes for 208 yards with no touchdowns and no interceptions against the Rams. That gives him a 96.7 passer rating for the season compared with a 104.1 mark for Smith.
Smith, who still leads the NFL with a .700 completion percentage, has not played since sustaining a concussion Nov. 11 despite being medically cleared two games ago.
Asked whether Smith could do anything to win back his job, Harbaugh kept his options open.
"Alex is not out of this," he said. "We've said it before: He's one of our guys. He's won us a lot of football games, and he'll be preparing himself to play in each of these games every single week.
"That's what his mindset has to be, as if he was the starting quarterback. So that's what we expect."
Jenkins, the first-rounder, was on the active roster but didn't play because Ginn remains ahead of him on the receiver depth chart. Harbaugh said Jenkins is "being integrated into the plan."
James remained inactive, with Brandon Jacobs emerging as the new No. 2 running back in the wake of Kendall Hunter's season-ending Achilles injury.
"(James) wasn't part of the plan yesterday, but that doesn't mean he won't be going forward," Harbaugh said.
Miami (5-7) at 49ers (8-3-1), 1:05 p.m. CBS