SANTA CLARA, Calif. — The NFL may be a quarterback league, but linebackers are grabbing the headlines for the San Francisco 49ers.

–Outside linebacker Ahmad Brooks caused more unnecessary drama on the team when he benched himself during the final three quarters of the 49ers’ 16-10 win against the New York Giants Sunday.

–Outside linebacker Aldon Smith, not coincidentally, made an impactful return to action in that game after sitting out nine games on suspension.

–Inside linebacker NaVorro Bowman is expected to join practice Tuesday for the first time since his horrific knee injury in the NFC Championship game against Seattle in January.

–Inside linebacker Patrick Willis was placed on injured reserve last week with a toe injury that requires surgery. He is out of the season.

–Inside linebacker Chris Borland, who wasn’t drafted until the third round this year because he is only the 5-foot-11 (248 pounds), was a big man in the victory over the Giants. His 13 tackles and two interceptions rendered moot any concern about the loss of Willis.

His teammates aren’t surprised.

“Yeah, he’s been playing amazing, stepping up,” Niners quarterback Colin Kaepernick said. “Our defense hasn’t missed a beat with him in there. He’s made a lot of plays and he’s someone, I think, since training camp and OTAs everyone was excited to see what he could do when he got the chance. And, I mean, he’s taking full advantage of it.”

But it was Brooks who created unnecessary commotion when he pulled himself from Sunday’s win in New York after just 12 defensive snaps because he was unhappy with how he was being used in combination with rookie Aaron Lynch.

This came one week after Brooks’ strip-sack on Drew Brees helped produce the 49ers’ win at New Orleans.

On Monday, coach Jim Harbaugh was less than forthcoming when asked about the Brooks issue.

“We’ve addressed it and had those conversations. Onward,” Harbaugh said, attempting to short-circuit any potential controversy.

Pressed to be more specific about the “conversations,” Harbaugh then slammed the door on the subject, blurting, “Yes, I can be specific. I can be very specific. It’s something I don’t want to share with you or share publicly.”

Brooks didn’t want to share his feelings, either, when approached after Sunday’s win.

“I’m good, man,” he said. “I’m not taking any questions today. Maybe later in the week. Not today. … We’re working through something.”

The game plan Sunday was for Brooks to share time with Lynch, who was moving from defensive right outside linebacker to Brooks’ spot on the left side because of the return of Smith on the right side.

Brooks started the game in Smith’s spot and played 12 snaps. But when it became clear late in the first quarter, upon Smith’s entry into the game, that Brooks would be splitting downs with Lynch on the left side, he balked at the idea and benched himself the rest of the game.

Seldom used Corey Lemonier got some of the snaps Brooks missed, playing seven downs.

When Bowman returns this week, he will be on the clock. The 49ers have 21 days from Tuesday — making December 9 the deadline — to join the active roster or he cannot play this season.

In the final game of one of the best seasons recorded by an NFL linebacker, Bowman’s knee was ruined even as he made a goal line tackle and forced a fumble and made a recovery that were not acknowledged, unless one counts a change in review rules this spring that would have legitimized his great play.

Bowman began working out with the 49ers’ training staff recently, but reported recurring pain in the knee. That prompted scheduling an MRI, which revealed no further damage.

The next step is to put Bowman back on the practice field with his teammates and try to get him up to game speed. Pain-free, of course.

Coming up barely short of becoming another linebacker making headlines is rookie inside linebacker Michael Wilhoite who, ostensibly playing Bowman’s position, recorded his first career interception Sunday. He and Borland became the first pair of 49ers linebackers to have interceptions in the same game since Rickey Jackson and Lee Woodall did it at Dallas on Nov. 12, 1995.

While all these linebacker headlines work themselves out the rest of this season, 49ers fans may wonder already what it will be like when the team opens training camp next year.

Will proven veterans Willis and Bowman regain their roles as starters and stars inside, or with Borland and Wilhoite have a say?

Of course Harbaugh wouldn’t touch that question, but he did lavish praise on the pair of rookies.

“Amazing performance by Chris,” he said. “The standard that Patrick Willis and NaVorro Bowman have set for inside linebacker play is at the highest level.

“Chris Borland, Michael Wilhoite, they are playing great, with a capital G, and rising to that level. It is great to see.”