SAN FRANCISCO -- Big-armed Colin Kaepernick fashioned an Alex Smith-like performance for the 49ers on Sunday.
Kaepernick took what the Miami Dolphins' defense gave him.
He completed a high percentage of his short passes.
He did not commit any turnovers.
And 49ers coach Jim Harbaugh even complimented Kaepernick's decision-making and his performance as a game manager.
In the end, Kaepernick put a stamp on the 49ers' 27-13 victory that was uniquely his own with a long scoring dash late in the game to clinch the victory at Candlestick Park.
Kaepernick last week broke Steve Young's 24-year-old franchise record with a 50-yard run against the St. Louis Rams. Young previously had the longest run from a quarterback in 49ers history with a memorable 49-yard gallop against the Minnesota Vikings.
On Sunday, Kaepernick peeled off another 50-yard run. This time, it went for a touchdown with 2:10 remaining when the 49ers were merely looking to pick up a first down and run out the clock.
The 49ers are 3-1 with Kaepernick after he took over for Smith when he suffered a concussion on Nov. 11 and remained in the lineup after Harbaugh anointed him as the so-called "hot hand."
San Francisco (9-3-1) maintained its 1 1/2-game lead over the Seattle Seahawks in the NFC West with three games remaining.
Kaepernick finished with a passing line that is not too different from what would ordinarily be expected from Smith. Kaepernick completed 18 of 23 passes for 185 yards with no touchdowns and no interceptions. His passer rating was 100.2.
"(I) thought he did a good job," Harbaugh said. "His ball security was better in the pocket, even though he did fumble one time. But I thought it was an improvement. (I) thought he managed the game well. Thought he did a good job in general."
Kaepernick said he was generally satisfied with the way he played.
"Yeah, I wish I had a few throws back and a few different decisions, but overall, yeah," Kaepernick said.
Kaepernick also finished with six rushing attempts for 53 yards and his fifth rushing touchdown of the season.
The 49ers have a new quarterback, but the overall identity of the team has not changed. The 49ers are still a squad that's defense-driven.
Six times the 49ers have lost regular-season games in Harbaugh's two seasons as head coach. Each time, the 49ers have responded with a huge defensive effort.
When Miami quarterback Ryan Tannehill hit tight end Anthony Fasano on a 3-yard touchdown at the midpoint of the fourth quarter, it represented the first touchdown the 49ers have surrendered in six previous games in which the 49ers were bounding back after a loss.
"This is a good Miami offense," Harbaugh said, "and we got the stop when we needed it."
After the Dolphins cut the 49ers' lead to seven points in the fourth quarter, Miami got the ball back. The Dolphins moved the ball to the 49ers' 35-yard line but Tannehill threw four straight incomplete passes.
"They were getting a couple of yards, spreading us out, dink and dunk and running a lot of screens," 49ers cornerback Tarell Brown said. "They did a good job of moving the ball, but we kept them out of the end zone and that's the most important thing."
Outside linebacker Aldon Smith had another big game with two quarterback sacks. The NFL sacks leader with 19.5, Smith is now just three sacks from Michael Strahan's league record with three games remaining.
"That would be a dream come true," Smith said. "You work hard and everyone wants that title. It would be a dream come true."
The defense prevented the Dolphins from tying the game, and then Kaepernick finished it off with his long touchdown run.
But for most of the game, the 49ers had a difficult time stringing anything together. The 49ers' offense went 96 minutes, 15 seconds without scoring a touchdown -- the equivalent of more than six quarters -- beginning in the first quarter of the 49ers' overtime loss last week to the Rams.
And, even then, the 49ers got a huge assist from special teams. C.J. Spillman recovered a Marcus Thigpen muffed punt early in the third quarter to give the 49ers the ball at the Miami 9-yard line.
Two plays later, Frank Gore scored on a 1-yard touchdown. It was Gore's 50th career rushing touchdown to match the 49ers' record set in NFL games that Joe "The Jet" Perry and Roger Craig previously shared.
The 49ers' best drive was a 13-play, 83-yard march that chewed up 7 minutes, 26 seconds. After Gore gained 19 yards to the 1-yard line, Anthony Dixon took it in from 1 yard for a touchdown that gave the 49ers a 20-6 lead.
Gore had 63 yards on 12 carries to eclipse the 1,000-yard mark for the sixth time in his eight-year career. Gore has 1,035 yards rushing through 13 games.
And the 49ers might have found a combination that will enable them to compensate for the season-ending injury to backup running back Kendall Hunter. Rookie LaMichael James made his NFL debut and gained 30 yards on eight rushing attempts.
"It's been a long time, but great things come when you're being patient," James said. "I'm just happy that I have the opportunity to go out there and compete and help the team win.
"At this level, those guys have been pounding for two or three months and today was my first day ever getting tackled. So I've got a little bit of an advantage, and I'll take it."
The 49ers deactivated disgruntled veteran Brandon Jacobs, and went with Dixon as the short-yardage back. Dixon had an 8-yard carry to set up Gore's touchdown, and Dixon produced a 1-yard touchdown on his other attempt.
Kaepernick was sacked four times -- once on a blown blocking assignment, once when he misread the defense and held onto the ball, and twice when Dolphins defensive end Cameron Wake defeated right tackle Anthony Davis in one-on-one battles.
Kaepernick fumbled once, but Davis recovered. The 49ers did not commit any turnovers, and they settled for David Akers field goals of 30 and 37 yards for their first two scores of the game.
The second-year player is now so firmly entrenched as the starter that there was no need for Harbaugh to be asked which quarterback would start next week at New England.