SANTA CLARA — The past two weeks have exposed flaws on the San Francisco 49ers’ defense that typically aren’t an issue for what has been one of the league’s top units.

Fixing those problems will be an even bigger challenge now that star defensive tackle Javon Hargrave is likely out for the rest of the season after partially tearing his triceps during Sunday’s loss to the Los Angeles Rams.

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Defensive Struggles in Recent Losses

During losses to Minnesota and the Rams the past two weeks, San Francisco has struggled to generate consistent pressure on the quarterback, failed to slow down the run game and been beaten for two big plays over the top.

It adds up to a team that is allowing a staggering 6.11 yards per play, which is the third-worst mark in the NFL this season and the fourth-worst in franchise history through three games.

“People are going to look at all the bad stuff that we’re doing when we are losing,” All-Pro linebacker Fred Warner said. “It’s not the standard that we have had since I’ve been here. But I see the things that are positive on tape and we just need to clean up things that are negative.”

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Adjusting Without Hargrave

They will have to do it without Hargrave, who signed a four-year, $81 million deal in 2023. He had an up-and-down first season with the Niners but was coming off one of his better games, with his five pressures against the Rams matching his high from any regular-season game last season.

After cutting defensive tackle Arik Armstead in a salary-cap move in the offseason, the Niners likely will go with two newcomers at defensive tackle in Maliek Collins and Jordan Elliott. Kevin Givens provides depth and San Francisco likely will promote another defensive tackle from the practice squad with T.Y. McGill the most experienced option.

“It’s just a group effort,” defensive end Nick Bosa said. “We have a lot of depth at that position.”

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Defensive Line Challenges

The Niners build their defense from the front to the back, investing heavy resources into the defensive line in hopes of controlling the game in the trenches.

That hasn’t happened so far this season. San Francisco is tied for 14th with eight sacks and ranks 19th in pressure rate at 21.3% of dropbacks, according to Sportradar. Over the previous five seasons, the Niners ranked tied for seventh in sacks and 11th in pressure rate.

Hargrave’s absence could force San Francisco to use more blitzes to create pressure.

“You would love to always get there with the front four,” coach Kyle Shanahan said. “That’s the goal. Getting there with four and having seven guys in coverage makes it a lot harder for the offense. But if you can’t do that, you’ve got to mix it up. … It’s a huge loss, losing Javon. Guys are going to have to step it up and when you don’t have the rush, then you’ve got to turn to other things schematically.”

Hargrave has nearly half of the team’s pressures from the interior — eight out of 18 — leaving a gap in the defense that needs more options outside of Bosa to generate pressure.

Defensive end Leonard Floyd was supposed to provide a boost this season after signing as a free agent. He recorded 39 1/2 sacks the previous four years. But he has one sack through three games this season and has generated only one pressure the past two weeks, according to Pro Football Focus.

The run defense also has been spotty, with the 4.52 yards per carry on pace to be the worst mark since Shanahan arrived in 2017 and more than a yard more per carry than the team allowed in 2022.

“We’ve had moments where we’ve been strong, but we’re not playing up to how we usually do,” Shanahan said. “We’ve got to make sure to get back to playing that way.”

Notes: QB Brock Purdy had no limitations at practice after coming out of Sunday’s game with a sore back. … TE George Kittle (hamstring) was limited after missing last weekend’s game. … LT Trent Williams (illness), WR Deebo Samuel (calf) and LB Dee Winters (ankle) didn’t practice. … San Francisco signed DL Shakel Brown to the practice squad. Brown spent most of training camp with the team.