NFL Media Insider Ian Rapoport reported Tuesday that Willis will undergo surgery to repair his toe.
"I promise you when I come back, I'll be better and stronger than I was before I left," Willis said Tuesday, via the team's official Twitter.
The Niners also appear to be in danger of not having the services of NaVorro Bowman this season. ESPN's Ed Werder reported Tuesday that Bowman is still having knee pain and is unsure when he will be cleared to return to practice. Bowman has not played a down since suffering a serious knee injury in the NFC Championship Game.