Wilson shot 1-under 69, and the pair carries an overall total of 11-under 199 into Sunday's fourth and final round at the El Camaleon Golf Club in Playa del Carmen, Mexico.
Van Pelt negated an earlier bogey with a birdie at 13 to grab sole possession of first place.
Both Van Pelt and Wilson birdied the 16th, but Wilson had to chip-in to maintain his spot at the top.
The pair is one stroke ahead of Briny Baird (67) and two ahead of J.J. Henry (69).
"So many guys are in it still," Wilson said. "If we start playing against each other, guys are going to steamroll right past us. It doesn't become really match play until there's a playoff."
2014: The Year in Music [PHOTOS]