Landing on injured reserve requires Sherman to miss at least the next three weeks under the league's adjusted rules.
The earliest Sherman could return would be for a Week 5 game against the Miami Dolphins on Oct. 11.
According to 49ers coach Kyle Shanahan, the hope is that Sherman's injury won't take any longer than the three-week minimum.
"He doesn't sound too concerned about it," Shanahan said. "He just is going to need a couple weeks we think, and maybe a little bit more. But hoping it's only three. That's why we put him on IR."
The loss of Sherman puts the Niners in a precarious position at cornerback, where veteran Jason Verrett is dealing with a hamstring injury and did not practice Wednesday. Making matters worse, Ahkello Witherspoon, who is the top candidate to replace Sherman, is in the concussion protocol.
With that in mind, the team elevated veteran Dontae Johnson, who played last week after being one of the team's two practice squad call-ups. He was promoted to the 53-man roster in a corresponding move.
The 49ers have not yet officially signed receiver Mohamed Sanu, who agreed to terms on a one-year deal Tuesday, as he goes through the COVID-19 testing protocols. If everything goes well with that, Sanu should be signed and on the field for practice on Friday. When that happens, the Niners will have to make a corresponding move because the roster is currently at the 53-man capacity after adding Johnson and Ken Webster, whom the Niners signed from the Miami Dolphins' practice squad Wednesday.
If Witherspoon clears the concussion protocol in time for Sunday's game against the Jets, he would start opposite Moseley on the outside with Williams in the slot. Johnson was one of the team's two practice squad promotions last week and played 19 snaps, all on special teams.
Sherman's injury came as a surprise after he played 78 of 82 snaps in the team's loss to Arizona on Sunday. The four snaps Sherman missed were at the end of that game when Arizona was kneeling to run out the clock.
On Monday, Shanahan did not mention any injury concerns about Sherman, who joins top receiver Deebo Samuel (foot) on injured reserve. Shanahan said Wednesday the team was still seeking more information on Sherman's prognosis at the time.
"We were still waiting to see how it felt on Monday, and later Monday afternoon, we found it was hurting a little more than he expected," Shanahan said. "Fortunately, we're able to do the IR to return, so hopefully it won't be too long."
Given Sherman's history with Achilles injuries, the Niners appear to be playing it cautious with any potential lower leg issues. Sherman suffered a ruptured right Achilles in November 2017, had a subsequent cleanup surgery on his left Achilles and then had sutures removed from his right Achilles after the 2018 season.
Sherman returned to form last season when he was named second-team All Pro with 61 tackles, 3 interceptions and 11 passes defended.
Asked whether the artificial playing surface at MetLife Stadium -- where the Niners play each of the next two weeks against the New York Jets and New York Giants -- weighed into the decision to place Sherman and Samuel on injured reserve, Shanahan indicated it wasn't a determining factor but was something they considered.
"If they were healthy enough to go, we wouldn't just not do it because of turf," Shanahan said. "But anytime that you have leg injuries, lower half injuries, going on turf doesn't help. Guys aren't excited for that. It's always a little bit harder on them."
Elsewhere on the injury front, Shanahan said tight end George Kittle (left knee sprain) would not practice Wednesday and would likely be held out Thursday and Friday, as well. Shanahan did not rule Kittle out for Sunday, though, noting Kittle's history of playing through pain.
"He fully expects to be there Sunday like he always does, and just like he always plays through the game when it happens, but we'll give him the whole week (off)," Shanahan said. "But Kittle is one that if he's ready to go on Sunday and the doctors say he's good to go, we have no problem with him going without practicing."
In more positive injury news, Shanahan said center Ben Garland (ankle) and receiver Brandon Aiyuk (hamstring) are expected to practice this week, and both have a chance to play Sunday, provided they make it through the practice week without a setback.