SANTA CLARA, Calif. — After coughing up a fourth-quarter lead to a division rival in the closing moments on Sunday afternoon, the San Francisco 49ers were left with an all-too-familiar emotion.

This time, it was the Seattle Seahawks storming down the field to score the winning touchdown with 12 seconds left, turning what seemed like a sure defeat into a 20-17 victory.

Given what the Niners were feeling, it might as well have been their Week 3 defeat to the Los Angeles Rams or the Week 5 letdown against the Arizona Cardinals.

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

What the 49ers are now is a 5-5 team teetering on the brink of a lost season. This loss dropped them to 1-3 in NFC West games and saw defensive end Nick Bosa suffer a hip and oblique injury that kept him out for most of Sunday’s second half and could linger into the coming weeks.

All of which would make the Niners’ path to a third straight divisional crown, or any playoff berth, substantially tougher.

The frustration Warner shares with his teammates isn’t just the record against divisional foes but how San Francisco has attained it. According to the Elias Sports Bureau, the 49ers have three divisional losses when leading in the final two minutes of regulation, which is tied for the most such losses by a team in a season since the 1970 merger.

San Francisco’s three late-game letdowns have come in just four chances, and the Niners are tied with the 2001 Carolina Panthers, 2000 Los Angeles Chargers, 1996 Baltimore Ravens and 1994 Washington Commanders as the only teams to have that many defeats in those situations on the résumé.

Losing a third game when leading in the fourth quarter also tied the Niners for the most such blown leads by any team this season, joining the Jacksonville Jaguars and Cincinnati Bengals. It all led to 49ers coach Kyle Shanahan touching on a similar message to what he has espoused after several losses this season (and even some wins).

“We had every opportunity to run away with that and put it away,” Shanahan said. “[We] missed a couple opportunities to do that and … let people hang around, that’s what happens.”

Indeed, the 49ers had multiple chances to build a big, perhaps insurmountable lead against the Seahawks. But a series of self-inflicted mistakes prevented that from happening.

Playing without tight end George Kittle because of a hamstring injury, the Niners were sluggish on offense, finishing with just 277 yards of offense, their lowest output in a game since Week 6 of the 2023 season. Their longest play of the day went for just 22 yards, tied for the second shortest for a game since Shanahan took over in 2017 (with 19 yards as the longest play in a 2020 loss to Washington).

More maddening for the Niners, however, was their inability to avoid penalties that wiped away multiple scoring chances. San Francisco racked up nine penalties for 54 yards, with seven of those infractions going against the offense. In recent seasons, the Niners have had no trouble overcoming such miscues, but this team hasn’t proved capable of the same type of in-game resilience.

“Obviously [in] years past, it’s like we put that behind us and play the next play,” quarterback Brock Purdy said. “Just because we had success the last couple years doesn’t mean just because something bad happens to us, we’re just magically going to make up for it. We’ve got to have the chip on our shoulder to go take it every single play, down and game. We’ve just got to get back to that mindset.”

While there are still seven games left in the season for the 49ers to rediscover what has made them successful in recent years, the clock is undoubtedly ticking as they prepare for a difficult two-game stretch with visits to the Green Bay Packers and Buffalo Bills. That they might have to do it without Bosa only figures to make the task tougher.

Bosa dealt with a right hip pointer and oblique issue all week that he said would make it “close” as to whether he would even play against the Seahawks. Bosa did start the game and had four tackles and 1.5 sacks before leaving early in the second half.

He injured his other hip and oblique when he brought Seahawks quarterback Geno Smith down for a sack with 9:26 left in the third quarter. Bosa stayed on the field for one more play before checking out and did not return. After the game, Bosa said he felt like he was “compensating” for the previously injured hip and oblique and lamented missing Seattle’s game-winning drive.

The Seahawks averaged just 3.3 yards per play when Bosa was on the field versus 6.1 yards when he was off it on Sunday. Seattle also scored all 20 of its points with Bosa off the field.

“Brutal,” Bosa said. “The most important time in the game for me to be out there, I wasn’t able to be. I hate missing time. That’s why I pushed through last week. Hopefully, it’s not too long [to be out].”