SANTA CLARA, Calif. - The 49ers' second-ranked defense that has missed a number of key players will have to finish the season without seven-time Pro Bowl anchor Patrick Willis.
Willis' toe that prevented him from playing in the last three-plus games will require season-ending surgery. San Francisco placed Willis on injured reserve Tuesday.
After suffering the injury in the second quarter of Oct. 13's game in St. Louis, Willis told the media he expected to return following the team's bye week. But he was unable to play in the loss 42-17 loss to the Broncos, and then practiced sparingly leading up to the team's 13-10 loss to St. Louis. He was a game-time decision and worked out on the field at Levi's Stadium before the game.
The linebacker said he initially suffered a strained muscle in his toe. "We thought it would be worse," he said at the time.
Willis suffered a setback at some point during his quest to get back on the field. Tuesday he said that he had been dealing with the toe injury for years, and that it had been exacerbated to the point where he thought he should shut it down for the betterment of his career.
"For me, I don’t look to play this game for just another year," he said. "I feel like I have five or six more years of great football left in my body. But unfortunately this toe was telling me otherwise. That’s the only thing that was weighing on my mind. And it started weighing on my mind for a while now. When it happened in the Rams game, I thought maybe I would be alright, but I knew it would be close. It just didn’t get better. So this was the route that was best."
Coming into the year knowing it would be without All-Pro linebackers Aldon Smith and NaVorro Bowman for the majority of the regular season, expectations for the team's defense were tempered.
But coordinator Vic Fangio has found replacements for those players and his unit remains one of the NFL's best. After Sunday's win in New Orleans, San Francisco's defense is the No. 2-rated unit in the NFL allowing 306 yards per game.
With Bowman recovering from his torn ACL and MCL in his left knee sustained in last year's conference title game, Willis made his first six starts along side Michael Wilhoite. And when Willis left in the first half in St. Louis, rookie third-round pick Chris Borland came in as the 49ers held on to win 31-17.
After a predictably rough outing against Peyton Manning and the Broncos in his first career start, Borland notched a team-leading 35 tackles over his last two starts at "Mike" linebacker in Willis' place.
"I’m truly proud of the way he’s playing," Willis said.
"...But as I was doing for NaVorro, Chris is doing for me now, but now he’ll have to do it a little while longer, until NaVorro’s situation is handled in the sense of him coming back."
Head coach Jim Harbaugh said Monday Bowman could return to practice this week, opening his 21-day window before he can be added to the active roster.
ESPN reported Tuesday Bowman was still feeling pain in his knee. He has been running and cutting in the final stages of his rehab before returning to practice. Harbaugh went on KNBR 680 Tuesday morning and said Bowman would undergo an MRI on the knee to gather more information before making a decision on his return to practice.
The deadline for Bowman's 21-day window to open Tuesday Nov. 18.
Willis said he is expecting to have the surgery to repair his toe in the coming days.
"We’re looking to do it soon, a lot sooner than later because in this situation the sooner we get it done, the sooner I can get back into rehabbing and get back to form. It’s going to take a while," Willis said.
The initial plan for Willis is to be recovered in time for the team's offseason program next spring and into the summer before training camp kicks off at the end of July.
"Everybody is different. I’m optimistic. I like to say I’m one of the hardest working guys in this universe, on this planet," Willis said.
The 49ers (5-4) travel to play the New York Giants Sunday and are a game out of the wild card standings behind Green Bay and Seattle, who are both 6-3.
The 49ers added running back Alfonso Smith to the active roster in conjunction with Willis' move to injured reserve. They also added linebacker Shayne Skov to the practice squad. Skov spent training camp with the 49ers and was added to the practice squad Sept. 15. He spent time with Tampa Bay's practice squad before returning to San Francisco's this week.