Wide receiver Demarcus Robinson suffered an ankle injury during the second quarter and was eventually carted to the locker room for further evaluation.
Shanahan confirmed that, as the 49ers feared, Robinson suffered a high-ankle sprain. He is a candidate for injured reserve.
"Any time it's a high ankle, we don't have a timeline, but high ankles in general are anywhere from three weeks at the best, which is very rare, to six weeks," Shanahan said. "So, we'll see how it goes, but most likely he'll be an IR candidate here."
Mike Evans update
Wide receiver Mike Evans exited the Dolphins game with a hip injury, which was initially considered a minor setback. Shanahan said Evans will need to be managed throughout the week.
The head coach also discussed the early chemistry Evans has developed with quarterback Brock Purdy.
"Mike's gotten a lot of work here in the last couple of weeks," Shanahan explained. "He's been able to practice each day since going down to Australia and last week. But no, I also think they're two really good players. Usually, when you have two really good players who are both instinctive guys, they gel together pretty fast."
Other 49ers injury updates
Rookie defensive end Romello Height broke his hand and will undergo surgery Tuesday. However, Shanahan has not ruled out Height playing Sunday against the Arizona Cardinals with protection over the injured hand.
"An outside chance to be ready for the game Sunday, but he needs to get surgery on that tomorrow," Shanahan said.
Rookie defensive tackle James Thompson Jr. was slow to get up after a play in the third quarter and eventually walked slowly to the locker room for further evaluation. He also suffered a high-ankle sprain and will likely need three to six weeks to recover.
Mykel Williams and Christian Kirk updates
Defensive end Mykel Williams began the season on the physically unable to perform (PUP) list as he continued to recover from the ACL injury he suffered last season. Wide receiver Christian Kirk started the season on injured reserve with a calf injury.
Neither player will return to practice this week, though both could return next week. Both are eligible for activation after Week 4.
"We're going to hold until next week on that," Shanahan said of Williams. "If we let him go, he was just going to do individual this week, so just don't feel the risk/reward of letting him go this week when he's just doing individual. We're going to try to hold him so we can hopefully replicate that on the side and get him going for practice, hopefully next week."
Regarding Kirk, Shanahan said, "He's not an option this week. He's not there yet, so we've got to wait another week on him at least."
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