LAS VEGAS — Patrick Mahomes was on the San Francisco 49ers’ minds even when they had the ball on Sunday.

Facing third-and-4 from the Kansas City Chiefs’ 9-yard line in overtime, Brock Purdy said he knew the 49ers couldn’t settle for a field goal because it would give Mahomes a chance to counter with the type of game-winning drive for which he’s become famous.

“You just don’t want to give him an opportunity to go down and win the game with a touchdown,” Purdy said.

That’s exactly what happened.

The 49ers’ third-down play was a good one. It called for Jauan Jennings, a strong contender for the game’s MVP award at that point, to start inside, then cut quickly back to the near pylon. He did, shaking his defender in the process.

“It looked like Jauan killed him, won pretty good,” 49ers coach Kyle Shanahan said afterward.

The problem is that no one blocked Chiefs defensive lineman Chris Jones, who’s both Kansas City’s best defensive player and someone who plagued the 49ers in their last Super Bowl meeting with the Chiefs. Right tackle Colton McKivitz put a hand on Jones, but moved to the outside to block defensive end George Karlaftis.

That gave Jones a free run at Purdy, who had to rush his pass and ended up throwing too far for Jennings. The 49ers settled for a 27-yard Jake Moody field goal and a 3-point lead. And that set the stage for what Purdy and the 49ers feared: A vintage Mahomes drive that went 13 plays, included a 19-yard Mahomes scramble and ended with a game-winning toss to a wide-open Mecole Hardman.

The score and resulting 25-22 victory left Mahomes with the MVP award and the 49ers exhausted, devastated and, for the second time in four years, ruing what could have been in a Super Bowl versus the Chiefs.

“When you have a good offense like the Chiefs do and what Mahomes can do, for us, it’s like, ‘All right we have to score touchdowns,’” Purdy said. “And we had opportunities to do so, I think. Shot ourselves in the foot just with penalties and the operations and stuff.”

For most of the game, the 49ers and Chiefs were virtual twins.

Both defenses were dominant early, taking the opponent’s best players out of the game. Defensive effort may have been an issue in the 49ers’ opening playoff games, but not on Sunday as players like Chase Young, Randy Gregory and Javon Kinlaw stepped forward with big plays that frustrated the Chiefs and held them to 6 points through nearly three quarters.

Mahomes’ favorite target, tight end Travis Kelce, had one catch for 1 yard at halftime. And Mahomes and Purdy had exactly the same modest passing total — 123 yards — at halftime.

The Chiefs defense, however, was even better at squashing their opponent’s star players. Receivers Brandon Aiyuk and Deebo Samuel were held to three catches each on Sunday despite Samuel being targeted a game-high 11 times. Tight end George Kittle had a key catch on fourth down in the fourth quarter but was held to 4 yards total. That fourth-and-3 throw in the fourth quarter also was influenced by Mahomes.

“That isn’t probably something normally we’d do, but thought it was the right thing in that situation,” Shanahan said.

The only true offensive weapons for the 49ers were Jennings, who had a passing and receiving touchdown, and Christian McCaffrey, who had a combined 160 yards of offense.

Jauan Jennings, celebrating his fourth-quarter touchdown catch, may have been in line to win the Super Bowl MVP had the 49ers hung on. (Patrick T. Fallon / AFP via Getty Images)

What’s more, the 49ers offense never could fully take advantage of Mahomes’ and Kelce’s modest starts.

Early in the third quarter, Mahomes was flushed from the pocket but found that Kelce was being blanketed by linebacker Fred Warner. He instead hoisted a pass to receiver Marquez Valdes-Scantling that was picked off by safety Ji’Ayir Brown at the Kansas City 44-yard line.

The 49ers had momentum, they had the crowd behind them and they had a perfect opportunity to build on their 10-3 lead. Instead Purdy threw an incompletion on first down, guard Aaron Banks committed a false start on second down and the 49ers had to punt the ball away.

“It was small things everywhere — all three phases,” fullback Kyle Juszczyk said. “We did things that weren’t characteristic to what we usually do as a team and I think in the end that’s what hit us, and it was too much to overcome.”

The 49ers also dealt with more attrition than the Chiefs.

They lost linebacker Dre Greenlaw in the second quarter when, while running onto the field following a punt, he tore his Achilles tendon. Right guard Jon Feliciano was injured late in the third quarter while Samuel (hamstring) and Kittle (shoulder) had to leave the game for stretches. During one critical sequence late in the fourth quarter, the 49ers were without defensive starters Greenlaw, Brown and Deommodore Lenoir.

As the 49ers weakened, the Mahomes-Kelce connection grew stronger. The tight end’s 22-yard catch and run at the end of the fourth quarter — he beat Warner, who had been strong against him to that point — set up the field goal that sent the game into overtime, and Kelce finished with 93 yards to lead all receivers.

“That’s probably the most disappointing thing about the loss,” Warner said. “Because we went into it saying that he wasn’t going to be the reason they beat us. And we were off on a couple of plays at the end there where he was running wide open over the middle of the field. That’s disappointing.”

Shanahan cited analytics as the reason he had the 49ers receive the ball to begin overtime. He figured the team that got the opening kickoff of the session might get a second possession.

“We wanted the ball third,” he said. “If both teams matched and scored, we wanted to be the ones who had the chance to go win (the game).”

The 49ers never got that chance. Their opening drive of overtime was their longest of the game — 7:38. That was followed by the Chiefs’ longest of the game — 7:19. The difference was that one ended in a field goal and the other in a touchdown.

After Mahomes’ big scramble into the red zone, tailback Isiah Pacheco ran for 3 yards and Mahomes hit Kelce for another 7 yards. That put the ball at the San Francisco 3-yard line with the clocking winding down in the first overtime.

The final blow came on a shotgun snap on which no one covered Hardman, who came in motion toward the formation but cut back to the outside. Both Warner and safety Logan Ryan were rushing toward Mahomes on the play.

THE CHIEFS ARE BACK-TO-BACK SUPER BOWL CHAMPIONS! pic.twitter.com/ZzfhTyUXg9

— NFL (@NFL) February 12, 2024

“I’m not sure,” Warner said of what went wrong with the coverage. “I’ve got to see it. I’m not sure who was supposed to be on (Hardman).”

The loss had a lot of the same themes as the one four years ago in Miami, including a blown lead and the inability to stop Jones and Mahomes in key moments.

The aftermath of this one, however, seemed worse. The locker room had a funeral-like quiet afterward. Shanahan gave only a brief postgame talk to his team, McCaffrey gave a clipped postgame interview and even the normally verbose Kittle’s session lasted just four minutes.

“Not a lot has been said,” Purdy said. “It just hurts. We have the team obviously to do it, to win the whole thing, and then to come up short like that. … The way things have been the last couple of years here, everyone wanted it so bad. So, I think we’re still trying to sort of gather our thoughts and everything right now. But everyone in that locker room loves each other, I’ll tell you that.”

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(Top photo of Brock Purdy being pressured in overtime by Chris Jones: Ethan Miller / Getty Images)