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Pepperdine led by 19 early in the second half, but San Francisco went on a 21-5 run that featured eight points from Lowhorn to pull within three, 58-55 with 12:14 to play.
The Waves retook a double-digit lead after consecutive steals and layups from Rico Tucker and Mychel Thompson to go up 70-60 with 8:27 to go.
But San Francisco tied it at 77 with 4:05 to play after a 3-pointer from Danny Cavic, a rebound and putback from Manny Quezada and a layup from Lowhorn.
Hernandez then gave the Dons their first lead of the game with a free throw that made it 78-77 with 3:41 to play.
Pepperdine (7-15, 1-5), has had its own coaching issues. Interim head coach Eric Bridgeland is 1-3 since taking over after Vance Walberg resigned on Jan. 17.
Pepperdine led by double digits for the last 10 minutes of a dominant first half.
Tucker followed a 3-pointer with a dunk and steal to put the Waves up 18-4 to open the game.
Thomas put Pepperdine up by 15 with a breakaway layup as the shot clock expired to make it 37-22 with 6:14 until halftime.
Cavic’s 15 first-half points kept Pepperdine reasonably close.
He scored seven straight San Francisco points to pull within 10, 27-17 with 7:47 to play, and made a hard-fought layup after several Don misses at the end of the first half.
“We haven’t had a great season,” Cavic said. “But no matter what we get to be part of his 800.”
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