"[Mostert's] going to have to go on IR," Shanahan said on Monday. "Erik Magnuson is going to have to go on IR also."
Mostert suffered an MCL injury while Magnuson sustained a severe foot sprain early in Sunday's game but continued through.
"[Magnuson] got a foot sprain in the first half," Shanahan said. "I think it was early second quarter, which we didn't know about it. He toughed it out, played throughout the whole game, and it's a pretty bad foot sprain, so he's going to have to go on IR. I was pretty amazed, I've got a lot of respect for that guy for staying out there and battling through it, especially with how short we were at tackles."
Mostert has carried the football six times for 30 yards this season. He also has five kick returns for 83 yards on special teams. Last season with the 49ers, which was his first regular season playing time with an NFL team, he had one carry for six yards.
Mostert, who was initially signed as an undrafted free agent by the Philadelphia Eagles in 2015, has spent time with six teams in his three NFL seasons. He was signed to the 49ers practice squad in November of 2016 following his release from the Chicago Bears and then promoted to the active roster on December 31, 2016.
Magnuson was signed as an undrafted free agent out of Michigan in April.
"He's earned our respect, a lot, I think everyone in our building," Shanahan said of Magnuson. "He made this team as an undrafted guard, center, an inside player, and he's been thrown in there to play tackle. And the game's not too big for him.
"Our line coaches told him just a couple of hours before kickoff that he was going to be starting and I think it surprised him a little bit. If you would have saw his face, you would have been pretty confident. I mean, the guy was fired up to get an opportunity, loves going out there and playing the game. It's not too big for him. He's not scared to fail."
The 49ers plan to look at replacement options on Tuesday.
"We've got a couple of guys on our practice squad who are options," Shanahan said. "And then we'll go through the people who are out there (free agents). Probably bring in a few guys for workouts tomorrow. I know those guys are working on that now. And then, just from a numbers standpoint, we're going to have to decide on someone. It will be between whoever we work out and the guys on our practice squad."
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