Harbaugh acknowledged that the road back to fitness would be a long one for the 25-year-old, but is confident that he has the mental strength to get back to his best.
"He's got healing ahead. He's got gruelling rehab ahead," Harbaugh told reporters.
"That is not the way that you would've wanted or foreseen his off-season to be after coming off what many have talked about - and deservedly so - of a defensive-player-of-the-year type of performance. Great year by NaVorro.
"Knowing what's inside of NaVorro Bowman, I have great faith in the human agency of NaVorro Bowman to continue to be great."
Bowman made 145 tackles, forced four fumbles and broke up seven passes during an impressive season for the 49ers.