With 58 seconds left Notre Dame's Jere Macura hit a layup and was fouled. His free throw and Torrian Jones' layup off an inbounds steal tied the score at 64-64.
The Irish then held WVU on its next possession, and Thomas was fouled, making both free throws.
WVU's Jonathan Hargett, who had a game-high 19 points, won contests against Tennessee and New Mexico on last-second three-pointers. He missed one with two seconds left.
Thomas was fouled on the rebound. He made one shot before Chris Moss' exasperation heave at buzzer missed to seal the Irish's fifth straight win in the series.
It was setup by Notre Dame's early second half shooting barrage. Down 36-21 at the half, the Irish hit six three-pointers in its first seven baskets to tie the game at 41-41.
The six-minute rally started with David Graves' three to end the first half. Matt Carroll hit three three-pointers and Chris Thomas added two in the 23-5 run. Thomas and Carroll finished with 15 and 14 points, respectively. Graves had 10.
Ryan Humphrey led the Irish with 18 points. His free throw with 14:16 to play gave Notre Dame its first lead, 42-41. The teams then battled over the final 14 minutes, which saw three lead changes and two ties.
The contest wasn't close early. West Virginia jumped out to a 16-7 lead as its perimeter defense smothered the Irish.
Notre Dame made only two of 13 three-pointers, 15.4 percent, in the first half against eight of 17 in the second half. West Virginia scored numerous times off turnovers and forced the Irish into bad looks as the shot clock ran down.
The Mountaineers, leading 20-11 at the 10:50 mark, went on an 8-0 run that pushed the lead to 17, the largest of the game. It was equaled again at 34-17 with 1:24 left on Lionel Armstead's driving bank shot. It was the senior's 1,000th career point.
Tyrone Sally scored 12 points and had eight rebounds for WVU. Armstead and Moss finished with 11 points, respectively.
Just two free throws were shot, both by Notre Dame, in first half. The Irish got to the line 20 times in the second half, making 10.
West Virginia has lost four straight and five of its last six after starting 6-2. Notre Dame is off to its best start since the 1985-86 team went 11-2.
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