Wake Forest will play fifth-seeded Pittsburgh (23-8) on Thursday in the second round.
Pat Connaughton scored 19 points for the 13th-seeded Fighting Irish (15-17), who lost their ACC tournament debut. The league newcomers shot 40 percent and had won at least one game in their previous five Big East tournaments.
Zach Auguste added 14 points, Eric Atkins had 13 and Garrick Sherman finished with 12 for the Irish, who briefly made things tense in the final moments when Atkins spun in a 3-pointer to make it 68-62 with 2:10 left.
Wake Forest guard Codi Miller-McIntyre then missed the front end of a one-and-one with 1:55 to play, but teammate Arnaud William Adala Moto grabbed the offensive rebound -- one of two missed free throws he rebounded in the final 2 minutes -- and Williams then hit two free throws with 1:52 to go.
Senior Travis McKie and Adala Moto each hit two foul shots, the last of which pushed the lead back to double figures at 74-64 with 1:22 remaining.
Notre Dame didn't get closer than eight the rest of the way. Thomas had given Wake Forest its largest lead at 62-48, hitting a fast-break layup through contact from Steve Vasturia -- and flexing both biceps to the crowd in celebration -- before converting the free throw that followed with 6:37 left.
Adala Moto finished with 12 points for Wake Forest, which claimed its first ACC tournament victory since a 114-112 double-overtime win over Georgia Tech in the first round of the 2007 event -- in what turned out to be Prosser's final victory.
The Demon Deacons went one-and-done in each of the past six years but used a big first-half run in just their third victory over an ACC team away from Winston-Salem in four years under coach Jeff Bzdelik.
Winning in the postseason might be an unfamiliar concept for Wake Forest, but certainly not for Williams -- a graduate transfer who played for the Robert Morris team that knocked off Kentucky in the NIT last March.
Williams scored 12 points in the first half and hit three 3-pointers from the same spot in the right corner. The last of them came midway through a 14-3 run and stretched Wake Forest's lead to 33-20.