Jones failed to score 20 points for the first time in 10 games. He had recorded nine straight 20-point games and would've tied a WVU record with one on Wednesday. He finished with 14 points and 12 rebounds.
The Mountaineers have now lost four of their last five games - all in Big East Conference play.
WVU was led by freshman point guard Jabarie Hinds who had 17 points in 31 minutes. He was 8-of-12 from the field.
"We're down right now, but we just have to bounce back," Hinds said. "We have to be more focused, and we have to spend more time on the court and get more shots up."
Player of the Game
4 free throws
"It's hard when Truck can't get to the rim, because his scoring allows for other people to get open and hit open shots," Jones said.
On the other end, Martin hit another three to go up by six with 51.7 seconds left.
Grant and Martin had 12 points apiece.
WVU outrebounded Notre Dame by two and turned the ball over just three times. But, the Mountaineers attempted just three free throws and shot just 24.1 percent from the field in the first half.
WVU and Notre Dame played continuously for the first six-and-a-half minutes, as the Mountaineers were able to jump out to a 5-2 lead on five straight points from Hinds before Cooley added his second layup of the game to make it 5-4.
The Mountaineers would not be able to take any more than a four-point lead early on, however, as they struggled to score in a game that put the Coliseum crowd to sleep.
With WVU up 12-10, Notre Dame went on a 9-0 run as the Mountaineers wouldn't score for 7:01 under Jones hit a short jumper off the glass.
With 4:15, Cooley went out with two fouls, but the Irish continued to find dominance as WVU struggled to score and defend.
After that initial 9-0 run, Notre Dame went on another 7-2 run including a final dagger 3-pointer from Martin when WVU's two seniors were caught guarding the same player in the paint.
It was the lowest-scoring first half for West Virginia since March 6, 2010, when WVU had 16 points vs. Villanova in a 68-66 overtime win.
In that first half, WVU shot just 24.1 percent while Notre Dame was 46.2 percent. WVU was out-rebounded by five, had six less second-chance points and had eight less points in the paint.
WVU found it much easier to score in the second half, and an 8-2 run in the first five minutes allowed the Mountaineers to cut the Notre Dame lead to just 32-26 forcing a timeout by Notre Dame head coach Mike Brey.
WVU would cut that lead to just four points on an acrobatic layup by Hinds to make it 38-34 with 8:51 to play when Brey called another timeout.
After the timeout, freshman point guard Gary Browne hit a layup and on the next possession Jones finished a short jumper to tie the game with more than seven minutes to play and ignite a crowd that was otherwise quiet before.
At that point, WVU had shot better than 60 percent in the second half.
The Mountaineers took a 41-40 lead, their first since it was 12-10 with 9:48 to play in the first half, on a three in the corner by Jones with 5:20 to play.
A Kilicli shot on the next possession forced Brey to call his second-to-last timeout with more than four minutes to go with WVU up 43-40.
From that point, Notre Dame found its shooting stroke and won the game.
The Mountaineers were just 2-of-16 from 3-point range. Bryant, Browne and freshman guard Aaron Brown were all 0-for-3.
There were just 9,258 fans in attendance at the Coliseum.