"He's going to end up having to go on IR," Shanahan told reporters. "He's going to be out six to eight weeks, so we ended up doing that."
Because of the required recovery time, the move will very likely end Colbert's season.
While rookie D.J. Reed replaced Colbert following Sunday's injury, Shanahan didn't dismiss the possibility that Jimmie Ward, if healthy, might move back to safety from cornerback. Ward is dealing with a hamstring injury and was inactive against the Rams.
"D.J. Reed will have the first chance up (to replace Colbert)," Shanahan said.
The 49ers head coach felt that Colbert was having one of his better games against the Rams.
"We had a challenge here in the last few weeks," Shanahan said. "I thought, in this game, he had covered sideline to sideline very well just running and hitting and made a real good play on the play he got hurt on, also. They tried to challenge us and go over the top, which you want the corner there on, but usually, the middle-third player will show up with the speed that Colbert has. He did, made a good play and unfortunately got hurt."
Colbert received his opportunity as a rookie last year due to injuries at safety, and now it will be Reed's turn to do the same.
"He's done some good things," Shanahan said of Reed. "He's still a rookie. He needs to play more. I know he'll have some learning curves as he does that but the game's not too big for him, and he's a guy we do believe in."
Shanahan also provided injury updates on several other 49ers players who were injured on Sunday.
"[RB Matt Breida] tweaked his ankle again but his strength is good," Shanahan said. "He'll be day to day. [WR Marquise Goodwin] tweaked his ankle. We'll recheck him on Wednesday. [S Jaquiski Tartt] had a stinger. We'll re-check him on Wednesday. [LB Reuben Foster] had a shoulder sprain. He should be good to go for practice Wednesday."
Shanahan also said that cornerback Richard Sherman will be re-checked on Wednesday. The veteran has been dealing with a calf injury.
"It's been wearing on him as the year has gone," Shanahan said. "Some weeks have been better than others. Last week was a bad week, and we'll see how he feels this Wednesday when he gets back in and is ready to go."
Wide receiver Pierre Garçon left Sunday's game multiple times with a knee injury. He will also be re-checked on Wednesday.
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