Gillis moved up from a tie for 12th place overnight and held a one-shot lead over Richard Johnson at eight-under 205. There were 18 players within four shots of his lead, and 28 within five.
'The winds were coming out of four different directions today, so it was quite a challenge,' said Gillis. 'You have to keep your wits about you.'
Johnson had a two-under 69 and was alone in second place at seven-under 206. On a tough day at Empire Lakes Golf Club, a 69 was good enough to put you in contention.
'I was getting annoyed because I was going nowhere,' Johnson said. 'But I looked up and I was right there. I didn't make many birdies today, but everyone was coming in the opposite direction.'
The overnight co-leaders -- Jon Mills, Chris Baryla and Jeff Wood -- all fell back significantly. Mills shot a 75 and was four shots back at 208, Baryla had a 77 and was at 210, and Wood tumbled seven shots off the lead following a 79.
Gillis improved his score for the second day in a row after shooting 70-68 in the first two rounds. He had six birdies and two bogeys, avoiding the mistakes that befell so many other players.
'Except for a three-putt on the sixth hole I played a pretty solid round,' said Gillis, who hit eight of 14 fairways and 14 greens in regulation.
Playing this week on a sponsor's exemption, Gillis struggled last year in his rookie season on the Nationwide Tour, placing just 110th on the money list. He has never finished better than third.
'I've actually played good all summer,' said Gillis. 'I just want to control my nerves and stay in the present -- all of those cliches you hear every week.'
Keoke Cotner bogeyed three of his last four holes and shot a 72 to fall into a tie for third place at six-under 207. He was joined by B.J. Staten (69), Matthew Jones (69), Bob Burns (71) and Jeremy Anderson (71).
There are three events remaining before the Nationwide Tour Championship.