"We'll know more by (Tuesday), but we're going to list him as questionable," Mariucci said.
Stokes underwent a Magnetic Resonance Imaging exam late Monday, but the team did not release the results. Stokes' status will be reavaluated Wednesday.
The eighth-year receiver was making a significant impact - his biggest of the season - during Sunday's 37-13 rout of the St. Louis Rams before he was injured.
Stokes scored the Niners' first touchdown in that game, burning St. Louis rookie cornerback Travis Fisher on a 13-yard scoring play. He later set up the Niners' second touchdown when he turned a short pass into a tackle-breaking 51-yard gain that got the 49ers out of a hole at their own 2-yard line.
It was on that play that Stokes was injured as he was being brought down by St. Louis' Dre' Bly.
If Stokes cannot play, Tai Streets would replace him in the starting lineup.
"It definitely would be disappointing for this team to lose J.J.," Niners quarterback Jeff Garcia said. "It's difficult to replace a starter. I think Tai Streets can do a great job in that place. But it doesn't allow us to do some of those things we were working on doing, like we did this week when we went to five-receiver sets and some of those things that we wanted to really elaborate on during this season. But now we'll be put into a different place until we really find out what's going on with J.J."