The Niners became the fifth team since the merger to lose three division games in a season after leading in the final two 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.”

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

San Francisco had their chances to change the outcome 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.

The 49ers got first downs on the first two plays, but then stalled when Christian McCaffrey got 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.

“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.

NINERS LOOSE BOSA

The San Francisco’ defense was formidable with the All-Pro pass rusher Nick Bosa, but turned to mush after he was forced to exit in the third quarter.

The 49ers were leading 10-6 with more than nine minutes left in the third quarter before Bosa left the game a play after he had a sack. Bosa was in too much pain to celebrate his take-down of Smith because he suffered an injury to his left hip. Bosa said the injury might have occurred because he was compensating for an injury to his right hip that had made him questionable to play.

The score came on a 14-play drive that was powered — literally, on one play — by Jennings. He had four catches for 42 yards on the 70-yard march, including grabs of 14 and 13 yards, respectively, when the 49ers were facing 3rd-and-11 calls.

On 3rd-and-11 from Seattle’s 21, Jennings busted through cornerback Josh Jobe’s tackle attempt at the 12 and carried three other defenders to the 8. On 2nd-and-goal, quarterback Purdy rolled left and found Jennings all alone for a 3-yard touchdown grab.

Purdy completed 21 of 28 passes for 159 yards with a touchdown and an interception. He completed 11 of 17 passes for 68 yards and threw his pick when he didn’t target Jennings.

Smith took advantage and methodically moved Seattle down the field. He only completed 11 of 16 passes for 91 yards with an interception (57.0 rating). After Bosa was sidelined, Smith completed 14 of 16 passes for 130 yards (100.5 rating) and had runs of 16 and 13 yards on Seattle’s game-winning drive.

Smith completed 7 of 8 passes for 54 yards before his game-winning scramble that ended in the front left corner of the end zone.

“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.”