Wilson's three-point play with 1:17 left put the Golden Eagles (2-2) up 59-55, the first two-possession lead for either team in over 4 minutes.
NJIT (1-4) closed to 59-57 with 23 seconds left on Daquan Holiday's free throws but sent Wilson to the line a second later where he pushed the lead back to four.
Marquette drew a charging call on Damon Lynn with 12 seconds left, and Steve Taylor Jr. made another free throw for the Eagles to cap the scoring.
Juan Anderson had 20 points and nine rebounds for Marquette and Taylor grabbed 12 rebounds.
Lynn had 13 points and Holiday added 12 for the Highlanders, who cut the deficit to one point three times in the final 5 minutes but never pulled ahead.