Down 49-40 with 14 minutes left in the game, the Cardinals used a 11-0 run to take their first lead since early in the first half.
The first run came late in the first half when Ball State erased a 14-point Pepperdine lead to tie the game at 30, but the Waves responded with 8 straight points to take a 38-30 lead into the break.
After Ball State tied the game on their second half run, the scores remained level for about 4 minutes until Ball State broke out two straight triples on the Pepperdine defense to control a 60-54 lead with under 6 minutes left.
However, the Waves would strike right back. Pepperdine's good defense combined with their ability to attack offensively allowed them to tie it up at 60 with a touch over 4 minutes left.
Less than a minute after the 4-minute TV timeout, Pepperdine would take their first lead in about 5 minutes of play, 62-61.
After trading baskets, Pepperdine's Shawn Olden would give the Waves a four-point lead on a clutch-three-pointer with under 1:45 left.
Then, after a huge stop by the Waves, Jeremy Major would convert a three-point play that would serve as the dagger into Ball State's heart.
The Waves would hit their free throws late to close out the victory.
Ball State's six-game winning streak comes to an end despite four Cardinals scoring into double figures, lead by 14 from Bo Calhoun.
Olden would lead all scores with 18 from off the bench for Pepperdine.
Ball State will travel to face Indiana State next in Terre Haute, while Pepperdine heads back home to play Louisiana-Lafayette.