Jimmy Walker, a two-time winner this season, posted a 5-under 65 to move into a share of second place. He is joined at 7-under-par 133 by Brendon De Jonge and Andy Sanders. Kevin Stadler and Chris Tidland each shot 65s to share fifth place at minus-6.
Thompson, who began his round three shots behind overnight leader Brad Adamonis, stumbled to a bogey at the par-4 second. He immediately atoned for that error with a birdie at the third.
The 25-year-old made it two in a row when his birdie try at the fourth found the bottom of the cup. Thompson then birdied the par-5 fifth to make it three in a row.
Thompson picked up another birdie at the seventh to make the turn at 5 under. He dropped in back-to-back birdies from the 10th before faltering to a bogey on the par-4 12th at Troy Burne Golf Club.
The Florida native parred 13 and 14 before catching fire down the stretch. He drained a birdie at the par-3 15th and came right back to birdie No. 16.
Thompson was not done yet. He made it three straight with a birdie at the 17th and ended his round with another birdie at the last to move three clear of the field.
'I did a good job of not getting ahead of myself, which you have a tendency to do when you're playing well,' Thompson said. 'I was flat out puring it today. I hit two 3-woods into par-5s that were frozen ropes.'
Walker, who won the BellSouth Panama Championship and Chitimacha Louisiana Open earlier this year, spread a bogey and two birdies over his opening nine holes. Around the turn, he birdied the par-4 10th. After running off four straight pars, Walker dropped in consecutive birdies from the 15th. He also closed with a birdie at the last to move into a share of second place.
'Everything feels real good at this point,' said Walker. 'I played a good, solid round of golf today.'
De Jonge birdied three of the first five holes on the back nine to start his round. He dropped a shot at the 15th, but birdied 17 and 18 to make the turn at minus-5.
The Zimbabwe native bogeyed the first and second, but came back to birdie the fifth. De Jonge ran off three straight birdies to close his round of 64.
'Today everything clicked. I hit the ball close all day and finally made a few putts,' said De Jonge, who was paired with college teammate Johnson Wagner. 'I couldn't have asked for an easier pairing,'
Sanders also got going on the back nine and bogeyed his first hole, the par-4 10th. He recovered by running off three straight birdies from the 13th. He parred the next four holes around the turn, before notching his fourth birdie at the second. He later birdied the fifth and seventh to move into a tie for second place.
Dave Christensen, Kevin Durkin, Steve Ford, Troy Matteson, Scott Petersen and Jason Caron share seventh place at 5-under-par 135. Wagner, John Douma, John Elliott and Stephen Gangluff are one stroke further back at minus-4.
Adamonis struggled to a 4-over 74. He now stands in a tie for 38th at minus-1. The cut line fell at even-par 140 with 66 players advancing to the final two rounds.