Jauwan Scaife scored 17 points and Jesse Berry had 13 for the Cardinals (8-12, 2-6 MAC), while Majok Majok bounced back from a scoreless first half to finish with nine points and a game-high 10 rebounds.
Bowling Green (8-13, 3-5 MAC) shot nearly 58 percent on its home floor at the Stroh Center. Jordon Crawford led all players with 19 points and eight assists, while A'uston Calhoun added 17 points and Chauncey Orr had 10.
Ball State whittled a 13-point halftime deficit to four on two occasions in the second half but could get no closer. The Cardinals shot better than 45 percent for the third game in a row but were out-rebounded for the first time in conference play, 30-26.
"I didn't think our sense of urgency was as high as it needed to be today," Ball State coach Billy Taylor said. "I thought our guys fought hard. We had some good stretches of basketball where we defended well or executed well offensively. We just didn't have a great sense of urgency like we needed to have."
Bowling Green shot better than 64 percent as a team in the first half with Crawford and Calhoun combining to make 11 of 14 attempts from the floor. The Falcons scored six points in the final 40 seconds of the half to turn a seven-point game into a 41-28 lead at the break.
Crawford did not start for Bowling Green for the first time in 46 games, but the Falcons' point guard made his impact felt when he entered after the first media timeout.
Ball State opened the second half on a 14-5 run and trimmed the Bowling Green lead to 46-42 on a pair of Matt Kamieniecki free throws just over five minutes into the half.
A 3-pointer from Scaife with 11:54 to play again cut the Bowling Green lead to four at 49-45, but Orr answered with a jumper on the other end for Bowling Green. Less than three minutes later, the Falcons pushed their lead to double digits on a fastbreak dunk from Calhoun.
"Our turnovers were leading to run-outs, and that's hard to overcome," Taylor said. "Our half-court defensive numbers were a lot better than what they were in transition. We gave up so many points in the open floor off of turnovers that it kind of skews our defensive percentages. I thought in the half-court we did a solid job."
Kamieniecki finished with six points and seven rebounds in 19 minutes off the bench, while Marcus Posley added seven points for Ball State. Berry led the Cardinals with four assists and four steals in addition to his 13 points.
Scaife reached double figures for the ninth time in the past 10 games, and the senior guard from Muncie is averaging 16.5 points per game during that stretch.
Ball State will now return home for two straight games at Worthen Arena. The Cardinals will host Ohio at 7 p.m. Wednesday and Western Michigan at 6 p.m. Saturday.