"He broke his pinky, had surgery this morning," Shanahan revealed. "We're hoping to have him back by Week 1."
Shanahan also mentioned that offensive lineman Ben Bartch has missed time this week due to knee irritation. However, he is expected to return soon.
In more positive news, safety Talanoa Hufanga received clearance from doctors on Thursday to increase football-related activities, which should lead to his return to the practice field. Hufanga and the 49ers remain hopeful that the safety will be ready for Week 1.
"We can push him a little bit harder," Shanahan said. "Not against players, but more football stuff, and those types of dynamic cuts and everything. Hopefully, he has a real good week of it, and we can talk about easing him into practice."
The 49ers have experienced several injuries in recent weeks, leading them to cancel their planned joint practices with the New Orleans Saints. However, the two teams will still meet on Sunday at Levi's Stadium.
"We've definitely been in this situation before with injuries," Shanahan said. "I thought we had good luck the last two years with them. I wouldn't say our luck's been horrible this year because there hasn't been a lot of long-term ones. ... I wouldn't say it was any more drastic than it's been some other years."