Warren, whose total of 19-under-par 196 broke the 54-hole record for this event by four shots, is seeking his first victory on the Buy.Com Tour.
Todd Barranger fired an 11-under 61 Saturday to break the course record at Cliffs Valley by a single stroke. He is tied for third place at 15-under with Jeff Freeman, Ken Green and overnight leader Stan Utley.
Warren, the 1997 NCAA Champion from Clemson, collected three birdies on the front nine but made his move on the back. He ran home a seven-foot birdie at No. 12 and followed it with a 10-foot birdie at 13. Warren's approach at the 14th spun two feet from the hole to set up his third birdie in as many holes.
Warren birdied 16 then took the lead with a 40-foot eagle at the par-5 17th. He finished with a bogey at the 18th, and when Klauk birdied the same hole, the margin was trimmed to one.
'I'm finally making some putts,' said Warren. 'Today was one of those days. This tour is a putting tour, you have to make putts to compete out here and that's what I did today.
'If I keep hitting it the way I am and making the putts, obviously I'll be fine. I'd like to hit it a little better so I don't have to rely on making 20- and 30-footers all day.'
Klauk, who established the old course record with a 62 Friday, posted six birdies and no bogeys Saturday for a 6-under 66.
'I know I needed a birdie on 18 to not have to shoot a really low round tomorrow and I did that,' said Klauk. 'Tomorrow is going to be a good day and definitely a good experience.'
Barranger, who carded 11 birdies Saturday, had a chance to shoot 60 but missed a 15-foot eagle try at his final hole.
'I'm not complaining about shooting a 61, but I definitely could have been in the 50s today,' said Barranger, who jumped from 39th at the start of the round to third. 'I missed a couple of makeable birdies and a good eagle chance on the last hole. But I got it going early today and got myself back in contention tomorrow.'
Scott Sterling is alone in seventh place at 13-under-par. Richard Barcelo, Todd Fischer and Andy Sanders share eighth at minus 12.
Kyle Thompson and former Heisman Trophy winner George Rogers captured the Pro-Celebrity title with a 28-under-par 187 total.
Former Georgia Tech star Bryce Molder and amateur partner Dan O'Connell won the Pro-Amateur division with a 33-under-par 182.
Full-field scores from the BMW Charity Pro-Am at The Cliffs