Wilson scored 17 points in the second half, including seven down the stretch, for the Golden Eagles (21-7, 12-4 Big East). His two free throws were the final points in the game.
Jerian Grant scored 21 points and Eric Atkins added 16 for Notre Dame (22-7, 10-6).
Jack Cooley, Notre Dame's leading scorer, had his minutes limited due to illness. He missed 9 minutes in the first half and 6 in the second.
The Golden Eagles' home streak is the second-longest active streak in the nation. South Dakota State's 30-game run was the best coming into Saturday's action. The Golden Eagles are 16-0 at home in 2012-13.
The Irish rallied from a 16-point deficit in the first half while the Golden Eagles went 5 minutes without a field goal. Zach Auguste's dunk pulled Notre Dame within 59-51 with 4:36 left.
Wilson's three-point play kept the Irish from getting any closer.
It was the 117th meeting and possibly the last regular-season conference game between the schools. Both are exploring multiple options for the 2013-14 academic year.
With Marquette ahead 41-27, Otule scored twice to open the second half, muscling his way through the paint. He banked in a shot and then made a hook shot along the baseline to give Marquette a 16-point lead.
Marquette led 41-27 at halftime after shooting 64.3 percent from the field and holding the Irish to 37 percent. The second half was more of the same, thanks to Wilson and Otule. The Golden Eagles ended the game shooting 59.6 percent while Notre Dame was at 38.3 percent.
Otule had 10 points in the first half on 5-of-5 shooting. He hit a short jumper after working his way down the lane with 2:52 remaining and gave Marquette its second 16-point lead. Atkins' 3-pointer brought the Irish to 39-27, but Vander Blue's fastbreak layup off a steal were the last two points of the half.
Notre Dame was without Jack Cooley, the team's leading scorer, for 9 minutes of the first half and 6 in the second. He was trying to play despite being sick. He went to the bench 2 minutes into the game and returned 9 minutes later with Marquette ahead 25-14. He started the second half.
Atkins, who had eight points in the first half, kept Notre Dame close in the second. His 3-pointer and three free throws and Tom Knight's putback off an Atkins' miss pulled the Irish to 56-46 with 9:20 remaining. A free throw by Grant cut the lead to nine with 7:30 to play.