The duo was tied for the lead at 21 under par when they made it to the closing hole. Elliott drove into the rough and hit his second 40 feet short of the hole. Warren, who eagled the 17th to match Elliott atop the leaderboard, found the fairway, then hit his approach 15 feet right of the hole.
Elliott lagged his birdie putt 2 feet left of the hole. Warren's birdie putt died left, but he tapped in for par. Elliott pulled his short par putt, giving Warren the victory.
'I told him walking off the tee, 'let's go make a couple of birdies because we played too good for this to end here,'' said Warren. 'I hate to see it happen that way.'
Warren posted a 6-under 66 on Sunday to come in at 21-under-par 267. Elliott managed a 2-under 70 and took his second runner-up finish of the year at minus-20.
Doug LaBelle II fired a 9-under 63 to get in the clubhouse at 19-under-par 269. Brett Wetterich (67) and Jeff Hart (68) shared fourth place at 17-under- par 271.
Warren trailed Elliott by three strokes to start the final round, but got back into the hunt with three birdies in a row from the first, including a long birdie putt from across the green at three.
He added a 12-foot birdie putt at the ninth, then birdied No. 10 to take the lead. Warren bogeyed the 13th to create a three-way tie between himself, Elliott and LaBelle.
Elliott made the first move out of the pack with a 22-foot birdie putt at the 16th. Warren got a great bounce from the rough, but failed to capitalize, missing the 7-foot birdie putt to fall one back.
At the par-5 17th, Warren hit a spectacular second shot to 4 feet. Elliott missed the green with his second, but pitched to 6 feet and made the birdie try to go two clear of Warren.
Warren ran home the eagle putt to match Elliott in first. Then Elliott missed the par putt at 18 and Warren all but secured his PGA Tour card for next season.
Warren won the Canadian PGA Championship two weeks ago and with the $108,000 first-prize check, he moved to fourth on the Nationwide Tour money list. That virtually assures him of a spot in the top-20, which gets him to the tour next year.
But Warren was still reeling from what happened on 18.
'I'm very pleased,' said Warren, who also won the 2002 BMW Charity Pro-Am at the Cliffs. 'We both played too well today and he played great all week.'