'It's been a long time since I've been on top. It's nice,' Waldorf said. 'But on a course like this, you've got to keep your focus. If you've got the opportunities to keep shooting for birdies, you've got to do it.'
Waldorf had his first 36-hole lead since the 2002 British Open.
'That was a real bunched leaderboard. This one's pretty bunched, too,' he said.
Wilson followed his opening 64 with a 69 for an 11-under 133 total at Tucson National. Jason Gore (66), Bob Tway (66), Scott Gutschewski (67), long-hitting Bubba Watson (67) and Jerry Kelly (68) were two strokes back at 10 under.
Waldorf started his day on the 10th tee and quickly went to 7 under with a birdie after missing a 12-foot eagle try. He bogeyed No. 11, his first bogey of the tournament, but reached 10 under with birdies on 12, 13, 15 and 16.
After the turn, Waldorf birdied two par-4s, the third and fifth holes, to reach 13 under. He three-putted on the par-3 seventh to drop back to 12 under.
'Today was trickier,' he said. 'There was a lot of wind in the afternoon. The greens dried out in the end, but I think I putted better today. It was a combination of good ball-striking and good putting.'
Wilson, the first-round leader, had a great start and reached 13 under at the turn after rolling in a 14-foot birdie putt on No. 9.
But that's just when the desert wind picked up and the greens dried out, and Wilson dropped out of the lead with a frustrating three-putt at the par-3 No. 12. He pushed his ball past the hole not once but twice en route to the double bogey.
'It was hard to hit that putt soft enough,' Wilson said. 'I hit it on the right line, but I shouldn't have chipped it where I did. And, yeah, the greens were definitely getting a lot drier by then.'
Wilson was in great shape after shooting a 31 on the front nine to reach 13 under. But then came the turn.
He scrambled for two pars after hitting a drive into the rough on No. 10 but still led by a stroke at the 12th. His tee shot stopped on the fringe 30 feet below the pin, but things seemed OK after he pitched 5 feet above the hole.
Yet he pushed the putt, running it 2 feet below the hole. Then he did it again, leaving himself with a 1-foot tap-in. The double bogey dropped Wilson to 11 under, but he got a stroke back with a birdie at No. 15.
'I'm happy with the finish,' he said. 'I played a little calmer coming in. I'm looking forward to the weekend.'
Waldorf, who won the last of his four PGA Tour titles in 2000, credited his recent work on his iron play for his strong performance. He made minor adjustments to the timing of his swing, and the birdies have accumulated: 14 so far to offset just two bogeys.
'Instead of 30 or 40 feet, I'm in there at 20 feet,' Waldorf said. 'When I hit a good shot, I'm inside 10 feet. I've hit a lot of greens this week but I've also hit it close a lot. Just a lot of good birdie chances.'
The cut was 4 under. ... Brent Geiberger eagled the par-5 No. 8 after hitting a 236-yard approach within four feet. ... David Duval placed an approach on No. 9 atop a townhome left of the green, taking a 7 on the par-4 hole.