Adam Schefter reports that the 49ers will turn to C.J. Beathard at quarterback now that Jimmy Garoppolo is out for the rest of the season. (0:47)

SANTA CLARA, Calif. -- The San Francisco 49ers and Jimmy Garoppolo's worst fears were confirmed Monday when an MRI revealed the quarterback suffered a torn ACL in his left knee late in Sunday's game against the Kansas City Chiefs.

Niners coach Kyle Shanahan said after the game the team feared Garoppolo had suffered such an injury but further testing was needed to be sure. That certainty came Monday afternoon, as the team announced the official diagnosis.

With that, Garoppolo's first season as an NFL starter comes to an end after just three games, and he and the Niners can do nothing but look to the future.

"I know I'm extremely excited about Jimmy being here next year," Shanahan said. "Jimmy is a very talented quarterback. He has played at a high level in the games that he has played.

"It's very unfortunate, I'm not going to sugarcoat it. It was hard waking up today. We were down, disappointed about it because we were looking forward to playing with Jimmy this year and going through the good and the bad that would happen knowing that he would benefit from all of it. Now we don't get to do that. I know Jimmy is really down about it and so are we, but it's still going to be all right."

The 49ers will place Garoppolo on season-ending injured reserve in the next few days as they juggle a roster that's dealing with multiple injuries.

As is customary with ACL injuries, Garoppolo is expected to wait until the swelling around his knee goes down before he undergoes surgery. That operation is expected to happen in the next week or two. Shanahan said initial indications are that Garoppolo suffered no further ligament damage in the knee, though he acknowledged there's a possibility that more could be discovered during surgery.

Typical recovery from an ACL injury takes about nine months, though Shanahan said the hope is that Garoppolo will be around for the start of the 2019 offseason program, even if he's not yet able to participate fully.

In the meantime, the Niners are set to begin tweaking their quarterback room to replace Garoppolo. C.J. Beathard will step in as the starter after getting more votes of confidence from Shanahan on Monday, and the 49ers intend to promote Nick Mullens from the practice squad.

In eight games, Beathard has completed 54.9 percent of his passes for 1,430 yards with four touchdowns and six interceptions for a passer rating of 69.2.

"C.J. is as tough and fearless as any quarterback I've ever been around," Shanahan said of the second-year pro. "He's got the arm talent to make every throw and he's extremely smart. And I know he's the type of guy that our team believes in also."

From there, Shanahan said the Niners will work out multiple quarterbacks Tuesday in search of additional depth. Among the names Shanahan noted will get a look are Tom Savage, T.J. Yates and Kellen Clemens. Matt Moore was another option Shanahan mentioned, though he wasn't sure if he would be working out.

As for the possibility of signing Colin Kaepernick, Shanahan stuck by what he said when asked about Kaepernick last year, when the coach didn't see it as a fit based on how he prefers to run his offense and the skill set of the quarterbacks already in place.

"It's kind of the same situation now," Shanahan said. "I always look into what style of offense I want to do, what style of offense we've been doing for the last two years, and when you start to get into these quarterbacks we're talking about, C.J. is our guy and we have Nick Mullens backing him up, so when you get into a third or fourth guy, whoever that is, you'd like to bring in guys who you felt you didn't have to change as much of your offense for."

Garoppolo's injury occurred with about 5 minutes, 35 seconds left in Sunday's game. On third-and-goal from Kansas City's 20, Garoppolo scrambled down the left sideline to the 7 before attempting to plant his left leg and turn upfield. His left leg buckled as he threw himself into Chiefs defensive back Steven Nelson.

Jimmy Garoppolo's 2018 season is over after three games because of a torn ACL. AP Photo/Charlie Riedel

After the game, Kansas City defensive end Justin Houston said Garoppolo erred in attempting to get more yards, leading to the injury.

On Monday, Shanahan said the play served as a reminder of why quarterbacks are coached to go out of bounds in that situation, even though there are multiple examples every week of quarterbacks risking their bodies and it working out for them without serious injury.

"I think that's something that Jimmy will probably look at different going forward because I know he'll remember this the rest of his life," Shanahan said. "Nothing against him, I think this happens with everyone. Like I said, you see it every Sunday and I think that's just a reminder for everyone why that is the obvious coaching point and why you need to stick with it."

Before the injury, Garoppolo was 20-of-30 for 251 yards with two touchdowns and no interceptions for a passer rating of 114.7. For the season, Garoppolo finished with 718 passing yards, five touchdowns and three interceptions for a passer rating of 90.0.

Earlier Monday, New England Patriots quarterback Tom Brady, the man Garoppolo backed up for more than three years before he was traded to the Niners last October, expressed his sympathy for Garoppolo on WEEI radio.

"It's a tough injury," Brady told WEEI. "I feel bad for Jimmy ... it sucks. You hate to see someone go down, someone I really like and have been friends with since the day he got here."

Brady is no stranger to ACL tears, having suffered one in Week 1 of the 2008 season. Coincidentally, that injury also happened against the Chiefs.

Niners running back Jerick McKinnon, who is out for 2018 with a torn ACL suffered the week before the start of the regular season, also offered support to Garoppolo on Monday via Twitter.

I am my brothers keeper! We will get through this together my brother 🙏🏾@JimmyG_10 — Jerick Mckinnon (@JetMckinnon1) September 24, 2018

Shanahan said the possibility of rehabilitating with McKinnon was one of the few things Garoppolo saw as a silver lining in talking to the 26-year-old Sunday night.

"It was the only good news that Jimmy and I could talk about on the plane," Shanahan said. "At least he's got a buddy to go through it with. Unfortunately, both of them are going through it but they are both in the same boat. ... They can talk a lot about it with each other, they can keep each other up, help each other when one is down."