Mathias Gronberg, who had held at least a share of the lead throughout the first four days of this event, carded a 2-under 70 to finish one shot back at 16-under-par 344 along with Dan Olsen.
Ellis was three shots off the lead to start the day on the back nine of the Crooked Cat course. He tallied his first birdie of the day at the par-4 11th and reached 14 under with back-to-back birdies starting at the par-5 14th.
The 33-year-old, who played on the PGA Tour under a Major Medical Exemption in 2003, caught fire on the front side with three consecutive birdies from the par-5 fourth to continue his charge towards the top of the leaderboard.
'The back is getting better and I'm getting healthier,' said Ellis.
Ellis stumbled with a bogey at the par-4 seventh, however, but he came right back with a birdie at the par-3 eighth to secure the outright lead.
'I want to try and play as well as I can tomorrow,' said Ellis. 'Everybody wants to play the PGA Tour. One more day and I'll be back there. I've got a little cushion to work with. I'll go at pins if I can but if I can't I'm just going to try and make pars.'
Gronberg also played Crooked Cat and collected four birdies and two bogeys to finish within reach of capturing medalist honors on Monday.
'I'm very happy with the position I'm in,' said Gronberg. 'I'm tied for second going into the last day of the PGA Tour Q-School. If you would have told me that going into the week I would have taken it.'
Olsen played the back side first at Crooked Cat and ran off three birdies over his last four holes to complete a round of 67.
Michael Allen posted a 3-under 69 to finish alone in fourth place at 14-under-par 346. John Riegger followed at 12-under-par 348 while David Branshaw was one shot further back at 11-under-par 349.
Roger Tambellini, John Maginnes and Wes Short shared seventh place at 10- under-par 350.
This six-round event, which is being contested on the Crooked Cat and Panther Lake layouts at Orange County National, concludes on Monday after which the top-30 and ties will be heading to the PGA Tour in 2004.