Van der Walt used a run during his second nine, the front at Dakota Dunes Country Club, to get to the top of the leaderboard. He wedged an approach to six feet to set up birdie at No. 3 and followed with a 10-foot birdie at the next hole to get to 12-under-par.
He hit a lob wedge to tap-in distance to set up birdie at No. 7, but dropped his only shot of the round at his closing hole, the 9th, missing an eight-foot par save.
'I guess when you're playing well, the ball bounces your way and you've got to take advantage of it,' said van der Walt. 'The key to this golf course is driving it well. The rough's pretty tough here so you've got to keep it in the fairway.'
Lee Rinker (65), Joe Daley (66), Bob Gaus (66), Darron Stiles (68) and Paul Claxton (70) are tied for third at 9-under-par 135.
Bates could have been tied for the lead, but bogeyed his 17th hole when he missed a 10-foot par save. He made seven birdies throughout his round, all from inside of 20 feet.
'I like to be up there, near the top, I just need to keep the ball in the fairway,' said Bates.
Van der Walt birdied four of his first seven holes on Friday to steadily climb the leaderboard.
'I'm not back in my van heading out, there's still some business to do,' he said. 'It's never won on Friday or even Saturday. It's won on Sunday afternoon.'
Sonny Skinner, David Kirkpatrick, Chris Couch and Rick Woodson round out the top-10 at 8-under.
The 36-hole cut fell at 2-under 142, with 70 players making it to the weekend.
Full-field scores from the Buy.Com Siouxland Open