David McKenzie posted a 69 to come in third at 11-under-par 205. Doug Barron and Dave Christensen were two shots further back at 9-under-par 207.
Warren was part of a five-way tie for the lead heading into the weekend at Whistle Bear Golf Club and made his claim for the leading position with two birdies over his first four holes.
He bogeyed the seventh, but drained a long birdie putt at the par-5 ninth to reach 10 under around the turn.
At the par-4 11th, Warren knocked his approach to 13 feet for a birdie and he roped his second shot to the par-5 12th within 5 feet of the hole for an eagle.
Warren then birdied the 13th to move to minus-14. He had another birdie chance at the 15th, but his putt lipped out. The 29-year-old parred his way in to hold a two-shot advantage with one round to play.
'This is one of the best golf courses we play. This is a championship golf course. We've got the rough, we've got the greens hard and fast and we've got the big crowds,' said Warren. 'It's definitely got a different feel to it than some others we play. At the beginning of the year one of my goals was give myself a chance to win golf tournaments on Sunday and I'd say this would be a chance.'
Cunningham birdied the third, but gave that shot back with a bogey at the very next hole. The 35-year-old then made his move with three consecutive birdies starting at the par-4 seventh.
He rolled in a 16-foot putt for a birdie at the 11th and kept on rolling with a birdie at the 12th. Cunningham then birdied the 16th to pull within one of Warren, but could not get up and down at the 17th en route to a bogey.
'I felt comfortable,' said Cunningham, who shot his second straight round of 67. 'Overall, I feel good. Just got to go out, keep picking out targets. We'll see what happens.'