Jerome Seagears, who hit four big free throws in the final minute, and Austin Johnson each had 10 points for Rutgers (11-8, 3-3 Big East), which is off to its best conference start since going 4-2 in 2003-04.
Gilvydas Biruta and Mike Pool added nine points apiece for the Scarlet Knights.
Notre Dame trailed the entire second half but pulled within 61-57 with 1:10 left. Seagears then hit two free throws and, after Atkins made 1 of 2, Seagears hit two more to make it 65-58 with 23.8 seconds remaining.
Trailing 39-31 at intermission, Notre Dame hit three straight shots to pull within 41-39 less than three minutes into the second half. Rutgers then reclaimed a comfortable lead with six straight points to go up 47-39.
The lead fluctuated between four and eight for the remainder of the game. Carter hit a big 3-pointer to put the Knights up 61-53 with 5:14 left. Rutgers would not score for the next 4:34, but Notre Dame could muster only four points as it missed the front end of a one-and-one, committed a turnover and missed two shots.
The Irish shot just 39.3 percent (11 for 28) in the second half while Rutgers hit just 33.3 percent (9 for 27) after both teams shot well in the first. Notre Dame finished 44.2 percent (25 for 52) overall and Rutgers hit 43.6 percent (24 for 55).
Notre Dame came out in a zone but switched to man-to-man as Rutgers hit 5 of 8 3-pointers in the first half.
After missing their first two shots, the Irish hit seven straight for a 16-13 lead. Rutgers responded with a 16-5 run to regain control at 28-21 and opened its biggest leads of the game at 35-26 and 37-28.
Both teams shot well in the half, with the Irish hitting 50 percent (12 for 24) while Rutgers was 53.6 percent (15 for 28).
The loss, Notre Dame's second straight, kept coach Mike Brey one win shy of 250 for his career with the Irish. Brey is also one win shy of tying Villanova's Rollie Massimino for fifth place all-time in Big East victories with a combined 123 regular-season and conference tournament wins.