Harbaugh feels the same when Smith is healthy, too.
Kaepernick looks to help extend San Francisco's unbeaten streak to six while making his third consecutive start Sunday at St. Louis.
Smith suffered a concussion while scrambling in the second quarter against the Rams on Nov. 11, but he remained in the game and led a touchdown drive before heading to the locker room.
Kaepernick finished that game and went 11 for 17 for 117 yards while adding 66 yards and a touchdown rushing as the teams played to a 24-all tie. Smith was forced to sit out a 32-7 victory over Chicago the next Monday night, and Kaepernick shined again.
He went 16 for 23 for 243 yards and two touchdowns, earning another start against New Orleans last Sunday despite Smith being cleared to play.
Kaepernick finished 16 of 25 with a TD pass while rushing for another score in a 31-21 win. Since replacing Smith against St. Louis, Kaepernick has a 104.1 passer rating while tossing three touchdowns and running for two more.
Those numbers are enough for Harbaugh to give the second-year pro another start, something Kaepernick appreciates.
''I don't know if it's a hot hand. Whatever you want to call it. I'm just happy I get to go back out there,'' Kaepernick said. ''It's a great chance to lead this team and show we're a great team and we can go into the playoffs.''
Harbaugh contends, though, Smith did not necessarily lose his job. Kaepernick simply has been playing well enough to deserve another shot.
"Both deserve it," Harbaugh said. "Alex over a long period of time, Colin by virtue of the last two games. What tips the scales is Colin we believe has the hot hand, and we'll go with Colin. And we'll go with Alex. Both are our guys."
Frank Gore, who ran for 83 yards and caught a 6-yard TD pass from Kaepernick last week, believes the 49ers (8-2-1) are in good hands no matter who is under center.
Gore has scored seven touchdowns as San Francisco has won four of five road meetings with the Rams.
"We've got two quarterbacks, and looking around the league a lot of teams can't say that," Gore said. "Alex won a lot of games. Kap has won the last two games.
"You're just going to be behind whoever coach says is the starting quarterback."
Rams coach Jeff Fisher has the luxury of seeing Kaepernick first-hand, unlike San Francisco's previous two opponents.
''When he's in the game, you have to be ready for a slightly different offense,'' Fisher said.
St. Louis (4-6-1) will be looking to build off a 31-17 road win over Arizona last week that ended a five-game winless streak. It forced a season-best four turnovers after not forcing any during its winless run.
"This game is really going to tell us who we are as a team," Fisher said. "They're the team to beat in our division. We got close but didn't get it done the first time, so it should be a good challenge for us."
Top wide receiver Danny Amendola had 11 catches for 102 yards in the first meeting with the 49ers, but he played only seven snaps last week and caught a 38-yard pass from Sam Bradford while being limited due to a heel injury.
He hopes to play this week.
''I guess we'll see,'' Amendola said. ''It's getting better each and every day, so it's just a matter of how I feel at the end of the week."
Rookie Chris Givens filled in nicely last week, finishing with career highs of five catches and 115 yards, including a 37-yard touchdown.
''I don't think there is a ceiling for him, I think he can be as good as he wants to be,'' Bradford said. ''He can stretch a defense. We can also throw him a quick screen pass and he can turn that into a big play, too.''
Steven Jackson rushed for 101 yards and a score against the 49ers in the first meeting and is coming off a season-best 139-yard performance against Arizona, helping St. Louis run for a season-high 173.
''He took over,'' Bradford said. ''I have seen it before. He gets that look in his eye and he is not going to be stopped.''
The 49ers, though, have allowed only 144 rushing yards over their last two games and rank fourth in the NFL, giving up 91.1 per contest.