ST. LOUIS — With the clock running inside 30 seconds and the 49ers possessing the ball at their 20-yard line, it appeared San Francisco would face an 11-point halftime deficit on the road against an upset-minded foe.

Colin Kaepernick and Brandon Lloyd had other ideas.

The quarterback and wide receiver hooked up on a stunning 80-yard touchdown pass with 14 seconds remaining in the second quarter, giving the 49ers momentum in their 31-17 victory over the St. Louis Rams on Monday night at the Edward Jones Dome.

It was the biggest play in a night full of them for Kaepernick, who completed 22 of 36 passes for 343 yards and three touchdowns.

“They had three timeouts and it was third down, but we wanted points,” 49ers coach Jim Harbaugh said, “so we took our shot. Kap made a perfect throw, Brandon did a great job with his double move and then finished the play.”

The touchdown enabled San Francisco to head for the locker room trailing only 14-10 despite having the ball for only 9:11 of the first 30 minutes.

“It was a huge spark,” San Francisco nose tackle Ian Williams said of the play. “Momentum plays are huge in a game like this.”

From there, San Francisco (4-2) controlled the second half. Kaepernick’s 11-yard touchdown toss to wide receiver Anquan Boldin with 9:58 left in the third quarter polished off a 12-play, 80-yard drive that gave the 49ers the lead for good at 17-14.

Kaepernick followed with a 22-yard dart over the middle to wide receiver Michael Crabtree with 13 seconds remaining in the third as the 49ers’ portion of a bipartisan crowd of 56,851 took over.

Meanwhile, the San Francisco defense clamped down on a St. Louis offense that rolled up 151 yards and 14 points in the first quarter. The Rams’ only points over the final three quarters came on a 38-yard field goal by placekicker Greg Zuerlein with 2:24 left in the game, cutting the deficit to 24-17.

St. Louis (1-4) got the ball back with 1:05 left at its 9-yard line and no timeouts left. San Francisco cornerback Dontae Johnson ended any hopes of overtime, intercepting quarterback Austin Davis and racing 20 yards for the clinching score with 53 seconds remaining.

Hassled most of the night by a pass rush that sacked him five times, Davis completed only 21 of 42 passes for 236 yards. He threw one touchdown pass and the one interception.

“You’ve got to win games in the end,” Davis said. “This one’s on me. I didn’t play good enough for us to win. We got off to a quick start, but we couldn’t do enough after that.”

The Rams started the game with an 11-play, 80-yard touchdown drive, scoring when running back Benny Cunningham ran a yard off left tackle on third-and-goal with 7:55 left in the first quarter.

St. Louis made it 14-0 with 53 seconds remaining in the quarter when Davis hit tight end Lance Kendricks with a 22-yard scoring strike off play-action. It came four plays after San Francisco tight end Vance McDonald fumbled to linebacker James Laurinaitis after a hard hit by free safety Rodney McLeod.

The Rams couldn’t add on to their lead, and eventually they lost their third consecutive game and dropped to 0-3 at home.

It was the third straight comeback win for the 49ers, but it came with a cost. San Francisco lost linebacker Patrick Willis (toe), left guard Mike Iupati (concussion) and backup free safety Jimmie Ward (quad).

“We had some mistakes early,” Harbaugh said, “but the guys showed their championship character. The guys set their jaw and got it done. This was a hard-working win.”

What the 49ers said:

“It’s a long game. The defense buckled down after their early TDs and played great. We have a lot of stuff to improve on.” — Left tackle Joe Staley.

What the Rams said:

“I will have to look at the film to see what I can do better and learn from this.” — Quarterback Austin Davis.

What we learned about the 49ers:

1. Even though the defense continues to lose players to injuries, San Francisco keeps finding ways to shut down its opponents. Linebacker Patrick Willis (toe) and backup free safety Jimmie Ward (quad) left with second-half injuries, but the 49ers allowed just three points after the first quarter. St. Louis rushed for just 18 yards after halftime, and San Francisco unleashed a good pass rush, sacking young quarterback Austin Davis five times.

2. The running game needs to pick up a lot between now and Sunday in Denver. The 49ers rushed 30 times for 89 yards, with quarterback Colin Kaepernick helping those stats by scrambling three times for 37 yards. RBs Frank Gore and Carlos Hyde combined for only 52 yards on 27 carries as the offensive line failed to generate a consistent push. If San Francisco is one-dimensional next week, it will have little chance to win against Peyton Manning and Co.

–LB Patrick Willis (toe) left the game in the third quarter and didn’t return. His status for Sunday night’s game in Denver wasn’t known. One of the leaders of the San Francisco defense, Willis finished with three tackles.

–LG Mike Iupati (concussion) departed in the second half and didn’t return. His absence might have been a reason that the 49ers weren’t able to run the ball as they usually do, finishing with only 89 yards on 30 carries. His status for the Denver game isn’t known.

–FS Jimmie Ward (quad) left in the third quarter and didn’t play for the game’s remainder. If he can’t play Sunday night in Denver, it would hurt a secondary that needs everyone on deck in order to deal with Peyton Manning and the Broncos. Ward recorded three tackles Monday.

What we learned about the Rams:

1. The pass rush that was supposed to terrorize NFL quarterbacks hasn’t recorded a sack since the season opener against the Minnesota Vikings. While St. Louis got to Colin Kaepernick a few times, it couldn’t put him on the ground. The lack of sacks is killing the secondary, which can’t consistently cover receivers and is getting burned for big plays on a weekly basis. While the absence of defensive end Chris Long hurts, there is still more than enough talent on the front seven for this unit to play a lot better.

2. Quarterback Austin Davis was great in the first quarter, posting a perfect rating of 158.3 after throwing for 103 yards and a touchdown. However, San Francisco shut him down over the last three quarters by getting consistent pressure, sacking him five times and forcing him to hurry other throws. Davis completed 21 of 42 for 236 yards, throwing a game-sealing pick-six in the last minute. Davis is essentially a rookie disguised as a second-year pro, so he needs reps to improve.

–RB Tre Mason played in his first NFL game and showed flashes of brilliance, ripping off a 24-yard run in the first quarter that could have gone for a touchdown if he hadn’t run up the back of WR Brian Quick. Mason led the team with 40 yards on five rushes and also caught a pass for 12 yards. Don’t be shocked if he earns more playing time.

–LG Greg Robinson picked up his first career start Monday night, with Rodger Saffold moving to right guard and veteran Davin Joseph going to the bench. Robinson appeared to play well early but had trouble at times in pass protection. With the Rams a 1-4 team, Robinson, the No. 2 overall pick in this year’s draft, probably should start for the season’s remainder to accumulate the reps he needs to improve.

–DT Aaron Donald earned his first career start and finished with four tackles. Donald was the No. 13 overall pick in the draft in May, but he hasn’t made as big an impact as some figured he might. Like rookie LG Greg Robinson, Donald figures to play plenty over the year’s last 11 games so that the team can start to see some return on its considerable investment.