Patterson made 13 of 17 free throws - both career highs - and had seven assists. Jake White scored 20, on 9-of-13 shooting, for Omaha (9-6).
A 3-pointer by Garret Covington gave Western Illinois (7-5) its biggest lead, 71-55, with 8:58 left.
Smallwood hit a pair of 3s and Patterson scored seven points during a 25-7 run that gave Omaha an 80-78 lead with 1:26 to play.
Jabari Sandifer's layup tied it 24 seconds later but Western Illinois missed its final three field goal attempts and Patterson made 2 of 4 free throws to seal it.
Tate Stensgaard led the Leathernecks with a career-high 26 on 13-of-15 shooting.