Thomas sank 10 of his 13 shots from the field and the Demon Deacons (10-8, 3-3 ACC) used 13 second-half points from Codi Miller-McIntyre to erase a 16-point deficit and pull off the upset.
Travis McKie contributed 16 points and eight rebounds, helping Wake Forest rack up 51 second-half points en route to its fifth straight home win.
Rodney Purvis (18 points), Richard Howell and Lorenzo Brown (13 each) paced the Wolfpack (15-4, 4-2), who fell for the second time in three games.
Leading scorer C.J. Leslie was also limited to 13 points after encountering foul trouble.