Thomas caught a pass from Drew Brees on the Saints' opening drive 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.
In December, the NFL instituted a new policy that required teams to have a certified athletic trainer in the press box to monitor play and help medical staffs evaluate injured players. The change was prompted by the Cleveland Browns' treatment of quarterback Colt McCoy, who was not checked for a concussion during a game and was sent back in after sitting out just two plays. McCoy was diagnosed with a concussion after the game and did not play the rest of the season.
The hard hits piled up early in San Francisco's first home playoff game in nine years.
Niners center Jonathan Goodwin got tangled up blocking in front of screen pass to Frank Gore, leaving with a lower left leg injury with 7:33 left in the second quarter. Goodwin, who won a Super Bowl with the Saints two years ago, returned after Adam Snyder replaced him for one series.
San Francisco receiver and kick-return specialist Ted Ginn Jr. also limped to the locker room just before halftime with a left 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.
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 on the play.
Graham returned for New Orleans' next possession and caught a 14-yard TD pass from Brees in the second quarter.
Information from The Associated Press contributed to this report.