Warren's 54-hole total of 14-under-par 202 was two shots better than Dave Cunningham.
David McKenzie had a 69 to come in third at 11-under-par 205. Doug Barron and Dave Christensen were two shots further back at nine-under-par 207.
Warren was part of a five-way tie for the lead heading into the weekend and moved into the lead alone with two birdies over his first four holes.
He bogeyed the seventh, but birdied the ninth to reach 10-under at the turn. He made a birdie at No. 11 and placed his second shot to the par-five 12th within five feet of the hole for an eagle.
Jeff Klauk, Johnson Wagner, Kenneth Staton, John Morse and Scott Dunlap share sixth place at eight-under-par 208.