The team said Thomas would not return.
The hard hits piled up early in San Francisco's first home playoff game in nine years.
San Francisco receiver and kick-return specialist Ted Ginn Jr. also limped to the locker room just before halftime with an apparent right ankle injury. He missed one series in the third quarter before returning a punt and rejoining the offense only to get injured again.
Ginn left late in the third quarter with a right knee injury after getting jammed at the line of scrimmage. The team said his return was questionable.
Graham returned for New Orleans' next possession and caught a 14-yard TD pass from Brees in the second quarter.