The win was Van Pelt's first in nearly eight years on the PGA Tour.
"I guess there comes a point where you draw a line in the sand and say 'enough's enough,'" Van Pelt said. "I had enough good chances and hadn't got it done."
The two players had finished regulation play at 13-under-par 267 after Van Pelt closed with a 6-under 64 and Mallinger carded a 65.
Van Pelt won $720,000.
Jerry Kelly (65) took third place at 268. Dicky Pride (65), Jeff Quinney (67) and Jeff Klauk (67) tied for fourth, another stroke back.
Frank Lickliter, who had led after three rounds, shot a 73 and finished in a tie for 18th place at 8-under 272.