Villegas stands at 12-under-par 132 for the tournament, which is still playing catch up after a four-hour weather delay during Thursday's opening round. Play was suspended because of darkness for the second straight day and will resume at 9:10 a.m. (ET) on Saturday.
Craig Bowden was also at minus-12 when the round was suspended. He played the first 12 holes of his second round at 6-under-par to reach Villegas at the top of the leaderboard.
Bowden was among 70 players who were forced to pick up their balls when darkness settled in on Midland Country Club.
Kris Cox is currently alone in third place at 10-under-par 134 after shooting a 65 in his second round. Rick Price and Garret Willis share fourth place one stroke further back after rounds of 68 and 69, respectively, on Friday.
David McKenzie, who shared the first-round lead with Bowden at minus-6, stands at 5 under through 12 holes of his second round.
The 23-year-old Villegas endured a 33-hole stretch on Friday after play was suspended very early in his first round. But the long, trying day didn't affect the Colombian, who carded a bogey-free second round to climb the leaderboard.
Villegas recorded 15 birdies in his 33 holes on Friday. He will be looking for his first title on the Nationwide Tour this weekend, with his best-ever finish being a tie for second place at the first tour stop this year, the BellSouth Panama Championship in January.