Thomas caught a pass from Drew Brees on the Saints' opening drive Saturday and absorbed a vicious blow from Donte Whitner just short of the goal line. Whitner jarred the ball loose, and Patrick Willis recovered for the 49ers at their own 2-yard line.
The Saints didn't immediately have an update on Thomas' status.
Saints tight end Jimmy Graham also limped off the field after getting tangled up with Whitner earlier in the first quarter. Officials called a 23-yard pass interference penalty on Whitner for the play.
Graham returned for New Orleans' next possession.