Omaha (16-13, 5-8 Summit League) raced out to 25-11 lead less than 10 minutes into the game, but IUPUI closed the first half with an 11-0 run to head into the break trailing 35-34.
A jumper by Khufu Najee 31 seconds into the second half gave the Jaguars (6-24, 1-12) their first lead but, after trading buckets on the next two possessions for each team, Omaha rattled off 17 consecutive points to open up a 56-40 lead with just more than 12 minutes to play.
The Jaguars never got closer than 14 again, and Omaha led by as many as 27.
Justin Simmons scored 15 and John Karhoff added 13 for the Mavericks.
Ian Chiles led IUPUI with 20 points.