Hegner made a pair of free throws with 12 seconds left to put Creighton (10-12, 1-8 Big East) up 75-72.
D'Angelo Harrison's missed a 3-point attempt going the other way and Amar Alibegovic grabbed the offensive rebound. Alibegovic elected for two points with a 15-foot jumper, leaving St. John's (13-7, 2-5) down by one with four seconds.
Hegner made both free throws for Creighton with 2.3 seconds and Harrison missed a 25-footer off the back of the rim at the buzzer.
Millikin scored nine of his 17 points in the final 3:15, starting with a 3-pointer that gave Creighton the lead for good at 65-62.
Harrison had 18 points to lead the Red Storm. Jamal Branch added 17 but fouled out with 2:43 left.