Tjaart van der Walt and Billy Judah share second at minus-8.
Benepe dropped birdie putts at two and three and added two more at five and six, both from over 20 feet. He added a three-footer for birdie at the 9th for a front-nine 31.
Benepe struggled at the outset of his second nine. He missed a 12-foot par save at No. 11 and he missed the green short at the par-3 13th to card another bogey. He rallied with a 35-foot birdie putt at 14, a two-putt birdie at 16 and a 12-footer at the last to claim the outright lead.
'I'm just trying to play the best I can,' said Benepe, who needed only 24 putts to get around Hillcrest Country Club on Friday. 'I'm hitting most fairways and greens as well and I'm taking advantage of the par-5s.'
Van der Walt picked up an early birdie at No. 2 but it was later in his front nine where he made his move up the leaderboard. He carded three birdies in a row, starting at the 7th to go out in 32.
'I'm making the putts I need to make,' said van der Walt, who posted his second 67 in as many days on Friday. 'Early in the year I wasn't making them. I'm not thinking the ball in the hole, I'm just doing what I need to do.'
Judah began on the back nine Friday and was able to overcome a double-bogey at his 14th hole with a birdie at the last to share second.
Arron Oberholser fired the lowest round of the day with a 7-under 64 to finish knotted in a tie with Don Reese, Patrick Sheehan, Craig Bowden and one of the overnight co-leaders Michael Long for fourth place at minus-seven.
The remaining first-round leaders struggled on Friday. Rob McKelvey posted a 3-over 74 and is 32nd at 2-under. Charles Raulerson and Charles Warren each carded 5-over 76s and barely made the 36-hole cut, which fell at even-par 142.