SANTA CLARA — The San Francisco 49ers looked to be in prime position to close out a divisional game when the defense made back-to-back stops in short yardage to get the ball back with the lead in the final four minutes.

What followed was another fourth-quarter collapse that has left the defending NFC champion Niners in peril of missing the postseason entirely for the first time since 2020.

The 49ers lost 20-17 to the Seattle Seahawks on Sunday when Geno Smith scrambled for a 13-yard touchdown with 12 seconds remaining, marking the third time this season they blew a late lead in the fourth quarter against a division opponent.

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Frustration Mounts for 49ers

“It’s just infuriating, honestly,” linebacker Fred Warner said. “It’s not like us. But that’s what we’ve shown this year. Until we stop doing that, then that’s what we are.”

The latest loss for San Francisco (5-5) followed early season defeats to the Los Angeles Rams and Arizona when San Francisco led by double digits in the fourth quarter before allowing a late score.

The 49ers became the fifth team since the merger to lose three division games in a season after leading in the final tow minutes, according to the Elias Sports Bureau. The last team to do that was Carolina in 2001.

“We gave them a chance,” coach Kyle Shanahan. “I thought our defense played great all game until that last drive. We let them hang around and when you let people hang around, that’s what happens.”

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Playoff Hopes in Jeopardy

The loss leaves San Francisco in a three-way tie for second in the NFC West, a game behind division leading Arizona. But with three division losses and another in the conference, the margin of error is getting slim for the 49ers.

San Francisco had chances to change that and close out this game on both sides of the ball but fell short.

After stopping Zach Charbonnet on fourth-and-1 from the 37 with 3:56 to play, the offense had a chance to run out the clock or make it a two-score game.

San Francisco got first downs on the first two plays, but then stalled with Christian McCaffrey getting stopped for a 1-yard loss on first down, Brock Purdy missing Deebo Samuel on a second down pass and Jauan Jennings getting tackled well short of the first down on a third down catch.

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Offensive Struggles Prove Costly

“We have to be better,” left tackle Trent Williams said. “We have to execute better. We have to put more than 17 points on the board if we want to win a divisional game.”

That forced a punt and put the game on San Francisco’s depleted defense that was missing star pass rusher Nick Bosa, who left earlier in the second half with an injured hip and oblique.

Smith took advantage and methodically moved Seattle down the field. He completed seven of eight passes for 54 yards and had two long scrambles, including on the game-winning score.

“Brutal, brutal,” Bosa said about only being able to watch at the end. “The most important time in the game for me to be out there and I couldn’t be. I hate missing time.”