Bubba Watson also posted a 65 to jump into second place at 17-under-par 199. First-round leader Mark Wilson carded a 5-under 67 and is alone in third place at minus-16. Heath Slocum shot 65 to get to 15-under-par 201.
Gabriel Hjertstedt and John Cook both posted 65s to climb to 14-under-par 202. They share fifth place with David Branshaw (66) and Jerry Kelly (68) at Omni Tucson National Golf Resort.
Waldorf led by one entering the round and flew out of the gates. He birdied the second and third to jump to 14 under. The Californian ran in a birdie try on the fifth to touch off another string of birdies.
The 43-year-old sank a birdie try at the sixth, then made it three in a row with a birdie on seven to move to 17 under. Waldorf parred the eighth and ninth.
Waldorf then birdied the par-5 10th. The four-time winner on the PGA Tour parred six consecutive holes before sinking a birdie putt on the 17th.
'Obviously, a win would get my career back on track,' Waldorf said. 'It's been six years. The irons are really working for me right now. I feel like I can hit every pin.'
Waldorf owns the 54-hole lead for the 12th time in his career. He has gone on to win two of the previous 11 tournaments.
The big-hitting Watson drained his first birdie effort on the fourth. He came right back with birdies on five and six to move to 13 under.
Watson birdied the eighth to make the turn at minus-14. The Floridian picked up birdies on the 10th and 12th to keep climbing the leaderboard. Watson carded his final birdie on the 15th to end in second place.
'That means you're hitting the ball really well,' Watson said of having hit all 18 greens in regulation. 'It gives you confidence when you go to the driver, your irons, just with everything. And now I've gone three rounds without a bogey. That helps too.'
Waldorf was awed by his playing partner Watson's prodigious length.
'His shots go so far that they're hard to follow,' said Waldorf of Watson. 'But I think this course plays well to everyone, whether you're a short or long hitter. If you get on with your irons and putt, you have a good chance.'
Kirk Triplett had the low round of the day as he posted an 8-under 64. That vaulted him into a tie for ninth at 13-under-par 203. He was joined there by Doug Barron, Jason Allred, Eric Axley, Mark Brooks, Chris Riley, Jason Gore and Nathan Green.
Marco Dawson and Ted Purdy are one stroke further back at minus-12.