The Cardinals (4-4) placed four scorers in double figures, led by Francis Kiapway with 14, but managed only 10 points as a team over the final 14:30.
Darell Combs led IUPUI (3-5) with 21 points, while Matt O'Leary scored 20 on 9-of-12 shooting.
"I thought IUPUI played . . .
Ball State led 36-29 at the half despite hitting just 2 of 8 free throws and playing for a while without Franko House, who was plagued by foul trouble. Sean Sellers scored 10 first-half points, and the Cardinals shot 48 percent as a team.
"We came out in the second half, and I called two timeouts in the first six minutes," Whitford said. "We weren't the same team as we were in the first half, for whatever reason. We were just trading baskets. We hit some tough shots early, but I could sense our defense wasn't very good."
IUPUI began to chip away at the lead, using an 11-1 run to pull within one near the 10-minute mark. The Jaguars then grabbed their first lead of the second half on a 3-pointer from Combs with 7:16 to play and took the lead for good at 59-58 with 5:24 left.
Ball State could not rally, making only two baskets in the final six minutes as the Jaguars stretched out their lead, IUPUI shot 48 percent in the second half and out-scored the Cardinals 20-10 in the paint.
"Defensively, in the second half, I thought we fell apart," Whitford said. "As they started to make a run, some of our breakdowns on defense, there were no excuse for. It's a long season, and we have plenty of time, but we have some warts we have to correct. This is a really critical month for us to get better."
Moses recorded a double-double with 13 points and 10 rebounds, while Sellers and Tayler Persons both finished with 12 points.
Ball State will return to action Tuesday, hosting Bradley at 7 p.m.