Andy Sanders and Larry Rinker finished one shot further back at 17-under 199.
Heinen, who captured the 1994 Houston Open on the PGA Tour, was six shots off the lead at the beginning of the round. He wasted no time in picking up ground with a 12-foot eagle putt at the par-5 first.
The Louisiana native then made the first of four consecutive birdies at the fifth for a 30 on the front nine.
'When I shot 30 I felt like I was in good shape to shoot something really good,' said Heinen. 'I tried to stick with my game plan from there. I was hoping to shoot 63 or 64 to get back in it.'
Heinen was on his way to an even better score. He birdied the 12th and made his second eagle of the day two holes later at the 14th.
Heinen birdied the 16th and made it two in a row at the following hole to equal the 18-hole course record originally set by David Lebeck at last year's event.
'I've been playing really well and have been feeling like I've been leaving a few out there. Today, I got a few of those back,' said Heinen. 'I hit the ball just as good today as I did the first two days, I just made four or five more putts today.'
The two-time All-American at the University of Louisiana-Lafayette has spent time on both the PGA and Buy.Com Tours. He came close to winning his second PGA Tour event at the 1995 Freeport-McMoRan Classic but lost on the second hole of a playoff to Davis Love III.
Raulerson, who played his college golf at Louisiana State University, managed two eagles of his own but struggled to keep pace with Heinen. The 38-year-old ran into trouble with a double-bogey at No.13, the same hole he double-bogeyed in the second round.
'It's going to be an old-fashioned Louisiana shoot-out tomorrow,' said Raulerson, who will play alongside Heinen. 'It's the Cajun's against the Tigers. It'll be a lot of fun.'
Steven Alker closed out an up and down round that included a double-bogey at the par-four ninth with a stretch of three consecutive birdies. The New Zealander, who is playing his rookie season on the Buy.com Tour, carded a 69 to finish alongside Keoke Cotner and Hunter Haas at 16-under 200.
Mark Hensby and Marco Dawson were both knotted at 15-under 201 while 2000 winner Rob McKelvey was one shot further back at minus-14. He was joined by Wes Short, Anthony Rodriguez and Jason Gore.
First-round leader Roland Thatcher was part of a larger group at 13-under 203 that included 1996 Bay Hill Invitational winner Paul Goydos.
Full field scores from the Louisiana Open