Per NBC Sports Bay Area's Matt Maiocco, Thomas won't return to the contest.
It appeared Thomas was inadvertently kicked in the face by a cleat, per 49ers reporter Joe Fann.
Thomas suffered a low-grade MCL sprain last season, but he was otherwise healthy and appeared in 14 games during his inaugural NFL campaign.
Operating as one of the 49ers' bookends along the defensive line, Thomas logged three sacks and 41 total tackles while playing 61.2 percent of San Francisco's total defensive snaps, per Pro Football Reference.
Should Thomas miss time, the 49ers will lean on Arik Armstead and Ronald Blair to collapse the pocket and contain the edges of their defensive line.