The 36-year-old Englishman, who shared the first-round lead with Fran Quinn, stood at 9-under 133 overall at the TPC Wakefield Plantation.
Jonathan Fricke fired a 5-under 66 to move into second place at 8-under 134, while Quinn managed a 1-under 70 to fall into a share of third place with Brad Fritsch (69) at 7-under 135.
Six players were knotted another shot further back at 6-under 136, and there were 20 players overall within five shots of Owen's lead heading into the weekend.
Owen made more than $3 million playing on the PGA TOUR the last three seasons and is looking to get back there, saying after the first round Thursday that that's where he belongs.
Ranked eighth on the money list entering this week, Owen was already well on his way to a spot in the top-25 at the end of the season, which would guarantee him a PGA TOUR card for next year.
A victory this week would all but guarantee that happens -- and it would be a long time coming.
Owen has never won on any of the major tours he has played. He is the leading money winner among Nationwide Tour players who haven't already claimed a victory this season.
Friday, he was able to overcome a bogey at the 18th hole -- his ninth -- and a double-bogey at the par-three seventh by making six birdies, including back- to-back birdies on his last two holes.
'One bad shot and it cost me a double-bogey,' Owen described No. 7. 'It's frustrating. I had an 8-iron and we waited for a while on the tee and I just pushed it. I lost a bit of focus there, but other than that I played great.'
It marked the fourth time this season that Owen has held at least a share of the overnight lead.
'It's where you want to be,' he said.
The cut line fell at even-par 142, with 70 players making the weekend. Two players withdrew, and Craig Lile was disqualified for signing an incorrect scorecard. Lile would have missed the cut anyway.