Smith is now completely healthy from the concussion he suffered in that Nov. 11 game and has been medically cleared to play.
But he'll be Kaepernick's backup for the second consecutive week. Smith is uncertain what Harbaugh's decision means for him the rest of this season.
"I feel like the only thing I did to lose my job was get a concussion," Smith said.
Smith was playing some of the best football of his career when he was injured and left early in the second quarter of the 24-24 tie with the Rams.
He completed 7 of 8 passes with a passer rating of 143.8 against St. Louis, throwing for his 13th touchdown of the season on his final pass. The week before, Smith completed 18 of 19 for 232 yards and three touchdowns during a win over Arizona, setting an NFL record with a 94.7 completion percentage for a quarterback with a minimum of 15 attempts. He was named NFC Offensive Player of the Week for the first time two days later.
Smith ranks fifth in the NFL with a passer rating of 104.1 and leads the league with a 70.0 completion percentage.
"You kind of state your case with your play and I felt like I've done that," Smith said. "It's tough. It stings the most just because I really felt there was something special going on here and you sacrifice and invest so much time. I felt like I was playing good football. I have no idea what's going to happen from here. All I can do now is just prepare and get ready."
Smith was in limbo the past two weeks after suffering his concussion, practicing every day with the 49ers in a non-contact black jersey. The 49ers did not announce during either week who would be their starting quarterback until game day against Chicago on Nov. 19 and New Orleans last Sunday.
There's no uncertainty this week. Kaepernick, San Francisco's second-round draft pick last year, took away the starting job from Smith with strong performances in decisive victories over the Bears and Saints.
Smith has lost his starting job and dealt with injuries and adversity several times before with the 49ers. He was beaten out for the role in training camp in 2008 by journeyman J.T. O'Sullivan, then began the 2009 season behind veteran Shaun Hill before starting the final 10 games of that season.
In 2010, Smith was replaced as the starter by former coach Mike Singletary with Troy Smith for a key December game that decided San Francisco's playoff fate that season. The next week, Alex Smith began a string of 28 consecutive starts for the 49ers that ended after his concussion.
Smith had a 21-6-1 record in those games and played a significant role in San Francisco's rise back to prominence last year and continued success this season. Smith resurrected his career under Harbaugh, who took over as San Francisco's coach in 2011.
"Those (other seasons) are all in the past," Smith said. "For this one, you're in it right now. It's such a great team, such a great group of guys in this locker room. There's something special going on. It's a tough pill to swallow, for sure."
Smith said he was prepared for Harbaugh's decision and knew it was a possibility "just based off the last couple of weeks the way things have gone." Smith got the news during a conversation with Harbaugh earlier this week, when the coach explained why he decided to go in a different direction.
Harbaugh left open the possibility he could go back to Smith at any time.
"Alex is a class act all the way," Harbaugh said. "He'll prepare as if he is the starter. And that's what we would expect. And be ready to go in and play and contribute to this football team. We've got two quarterbacks that we feel great about as the starting quarterback. Anything's a possibility. I would assume nothing, or rule out anything."
Smith said he felt no resentment toward Harbaugh, nor did he try to talk the coach out of the change at quarterback.
"At this point, what's talk going to do?" Smith said. "I feel like he made up his mind, and he's not a guy that didn't put thought into it already. I don't get to make those decisions. That's what he gets paid to do. I play football. So that's what I'm going to continue to do. Continue to get ready, and then make the most of my next opportunity."
Around the league
Bears • Return specialist Devin Hester and guard Chris Spencer have been ruled out for Sunday's game against Seattle. Both players were injured in a win over Minnesota last weekend. Hester had a concussion and Spencer has a knee injury. The Bears were a banged up bunch after playing the Vikings, with running back Matt Forte, cornerback Charles Tillman and linebacker Lance Briggs suffering ankle injuries and guard Lance Louis tearing the anterior cruciate ligament in his left knee.
Jets • Tim Tebow was limited in practice again with two broken ribs, leaving the backup quarterback's status uncertain for the team's game Sunday against the Arizona Cardinals. Tebow was injured at Seattle on Nov. 11, played three offensive snaps the following week at St. Louis and was active but didn't play last Thursday against New England.
Packers • Cedric Benson will remain on injured reserve for the rest of the season after having surgery Wednesday on his sprained left foot. The running back was able to resume practicing last week after being placed on the injured reserve but designated to return list Oct. 10, and could have played as early as Dec. 9.
Steelers • Ben Roethlisberger practiced in a limited role Thursday and appears a long shot to return for Sunday's game in Baltimore. The lengthy list of issues still plaguing Roethlisberger more than two weeks after he sprained his right shoulder and suffered a dislocated rib in a 16-13 overtime win against Kansas City, however, suggests he's still a week away from giving it a go.
Texans • The NFL has reduced its fine on defensive end Antonio Smith for kicking Miami's Richie Incognito to $11,000. Smith was initially fined $21,000 by the league for kicking the Dolphins guard. Smith appealed, saying he was retaliating to Incognito's stepping on his right ankle during the season opener. He missed two practices the following week with soreness in the ankle.
Week 13 schedule
• New Orleans at Atlanta, 6:20 p.m., NFL Network
• Seattle at Chicago, 11 a.m.
• Minnesota at Green Bay,11 a.m.
• San Francisco at St. Louis,11 a.m.
• Carolina at Kansas City,11 a.m.
• Houston at Tennessee,11 a.m.
• Arizona at N.Y. Jets, 11 a.m.
• Indianapolis at Detroit,11 a.m.
• Jacksonville at Buffalo, 11 a.m.
• New England at Miami,11 a.m., Ch. 2
• Tampa Bay at Denver,2:05 p.m., Ch. 13
• Cleveland at Oakland, 2:25 p.m.
• Cincinnati at San Diego, 2:25 p.m.
• Pittsburgh at Baltimore, 2:25 p.m., Ch. 2
• Philadelphia at Dallas,6:20 p.m., Ch. 5
• N.Y. Giants at Washington, 6:30 p.m., ESPN