The Eagles led most of the way and Ryan Anderson scored four straight points for Boston College to tie the score at 73 with 35 seconds left, but Atkins took the inbounds pass and drove the ball up the court and hit the game-winner to finish with 24 points.
The Irish (12-10, 3-6 Atlantic Coast Conference) won for just the second time in their last eight games. Boston College (6-15, 2-6) fell to 1-7 on the road.
Both teams squandered chances to win in regulation. The Eagles had a chance to open a three-point lead with 7 seconds left, but Olivier Hanlan missed the front end of a one-and-one, ending a streak of 13 straight made free throws by the Eagles. Atkins then drove the length of the court and appeared to lose control of the ball, but Hanlan was called for the foul with 0.7 seconds left.
Atkins tied the game with his first free, throw, but missed the second.
Atkins scored 16 of his 24 points in the second half and overtime to lead the Irish to the victory. Pat Connaughton added 17 points and nine rebounds and Zach Auguste and V.J. Beachem finished with 10. Beachem scored all his points after intermission, including a 3-pointer early in overtime that gave the Irish their first lead since the first half, as Irish reserves scored 15 points in the second half after being held scoreless in the first.
Anderson led Boston College with 21 points, Lonnie Jackson had 15 and Joe Rahon added 11. Alex Dragicevich, who played for Notre Dame before transferring following his sophomore season in 2012 because of a lack of playing time, made his first start for BC since Dec. 28. He was booed by the Notre Dame student section every time he touched the ball, and when he finally hit a 3-pointer late in the first half, his teammates on the bench stood up and cheered.
Boston College led by as many as nine points in the second half, but the Irish closed to within a point twice before finally tying the score at 58 on a three-point play by Atkins with 3:32 left. After trading baskets, Boston College scored four straight points on a layup by Jackson and a pair of free throws by Rahon. Atkins then hit a 3 for Notre Dame with 47 seconds left to cut the lead to 64-63.