The 26-year-old Thomas missed 10 games last season because of a severe left ankle sprain. He gained 269 yards rushing with two touchdowns in the six games he played.
Thomas, who in 2007 made the Saints' roster as an undrafted rookie free agent out of Illinois, emerged as the club's top rusher in 2008 and 2009.
He also has been effective on screen passes, on which he scored touchdowns in both the NFC title game and Super Bowl two seasons ago, and has filled in on kickoffs when needed.
The Saints did not release financial terms of the deal, which was announced on Thursday.