Frank Gaines led IPFW with 17 points on 7-of-13 shooting from the field, while Mario Hines scored 13 and Joe reed 10.
Pierre Bland and Michael Kibiloski each pulled down four rebounds for IPFW, while Isaiah McCray gave out a game-high three assists.
The Mastodons (9-12, 2-5 SL) jumped out to a 4-0 lead in the game, and pushed the lead to 18-9 with just under eight minutes to play in the opening stanza.
The Kangaroos chipped away at the lead, using an 8-0 run to cut the gap to one, and took their first lead of the half on a Thomas Staton jumper with 48 seconds in the period.
IPFW took a 25-24 lead with 31 seconds left on a Hines three-point play, but a Estan Tyler jumper at the buzzer sent the visitors into the locker room with a 26-25 lead after the first 20 minutes of play.
The late first half momentum carried over for Kansas City (6-14, 3-5) into the second half, as the visitors scored the first five points of the period to take a six-point, 31-25 lead.
The lead remained at six with 18:28 to play before the Mastodons rattled off 10 of the next 13 points to lead by one at 37-36. the lead changed hands five times in a two minute span, before UMKC pushed ahead by three at 44-41.
IPFW took a two-point lead on back-to-back three-point plays by Reed, and led by three after a three-pointer by Kibiloski with 6:01 left on the clock. A Gaines lay-in with 5:16 to play provided the last basket for the Mastodons, as the Kangaroos ended the game on a 7-1 run to claim the four-point win.
Estan Tyler scored a game-high 19 points for Kansas City, while Staton scored 14, and Trinity Hall and Kirk Korver each added 11.
The Mastodons will host Western Illinois Thursday at 7 p.m. at the Gates Sports Center.