Mike Tschetter, Tom Carter and overnight leader Chad Campbell share third place at minus-12.
Fischer used two separate runs of three birdies in a row to jump to the top of the leaderboard. He made three in a row starting at the second and added two more on the front at Nos. 6 and 9.
His birdie at the ninth was the start of the second trio of consecutive birdies. Fischer added birdies at Nos. 15 and 17 but his play at the closing hole was what preserved his lead.
Fischer drained a 12-foot par save at Mission Dorado's finishing hole to remain alone in first.
Click here for Todd Fischer's scorecard.
'My bad shots right now aren't that far off line,' he said. 'I'm driving the ball fairly well and hitting it 10-to-15 feet and running some in. This week, you've got to make putts. If you don't, you're getting passed.'
Fischer is a Monday qualifier who has not found a permanent home on the Buy.Com Tour. He has entered five tournaments in this fashion and has survived the cut all five times.
'My goal is just to find something a little more permanent,' said Fischer, who finished fourth at the Carolina Classic. 'I've bounced around a little, playing here and there. I'd love to be out on the PGA Tour of course, but if not, I'd like to play here full time.'
Patterson, who played his way on Tour this season, carded nine birdies and one bogey, at the par-4 16th, en route to a 64.
'I have to say I'm finally getting more comfortable out here with the birdie-fests,' said Patterson, who tied for fourth at the tour's opening tournament, the Florida Classic. 'It seems like every week you've got to get to 15- or 20-under par just to have a chance.'
Phil Tataurangi (67), Rod Pampling (68), Jeff Sanday (68) and Billy Tuten (65) are knotted in sixth place at minus-11.
Casey Martin survived his seventh cut of the 2001 campaign with a two-day total of 8-under 136.
The 36-hole cut fell at 6-under-par 138, making it the lowest cut on tour this season and the lowest since last year's Buy.Com Wichita Open, where the cut also fell at minus-six.
Full-field scores from the Buy.Com Permiam Basin Open