Thompson eagled the par-5 18th in regulation to post a 5-under 67 and get into the clubhouse at 17-under-par 271. He was joined there by Matthew Jones, who birdied the last to shot 66, and Jon Turcott, who shot 69.
Turcott was eliminated on the first playoff hole, the par-5 18th, as he made par. Thompson and Jones both two-putted for birdie on the hole to advance.
They played the 18th again, and again Thompson made birdie as he got up and down from a greenside bunker to secure his second win of the season.
'It's been a crazy year. I have two wins, and a bunch of top 25s,' said Thompson. 'So I either miss the cut or I finish top 25. Ideally, that's the way to do it. So you have some weekends off. I had one year on tour out here where I made 17 cuts, but only $67,000. That drives you crazy because you are playing so well and not cashing in on the weekends.'
Brendan Pappas (68) and Brad Elder (71) shared fourth place at 15-under-par 273. Peter Tomasulo and Mike Heinen were one shot further back at minus-14.
Thompson, who won earlier this year at the Rex Hospital Open, stumbled out of the gate with a bogey at the first. He rebounded with three straight birdies from the third.
The 28-year-old Thompson dropped another shot at the sixth to slide back to 12-under. He recovered that shot with a birdie on the par-5 ninth at Shadow Hills Country Club.
Thompson dropped in back-to-back birdies from the 14th to get within two of the lead. He closed with a 60-foot eagle putt at the last to join Jones in the clubhouse at 17-under.
'It's such a relief and a weight off my shoulders,' said Thompson, who earned $85,500 and moved from 27th to seventh on the money list. 'Back-to-back years I came about $5,000 short of earning my card. The year I finished 22nd on the money list, I three-putted on the final hole of the Tour Championship to lose my card. But everything happens for a reason. I firmly believe in that.'
Jones opened with three birdies in the first five holes. He turned at 15-under thanks to a birdie on the ninth. Jones birdied 13 and 15 to get to 17-under. He dropped a shot on 17, but came back with a birdie on 18 to get into the playoff.
Turcott was in the penultimate group and had a chance to win in regulation. After a birdie on the second, he faltered to a bogey at the fourth. He drained consecutive birdies from the sixth.
At the 10th, Turcott made birdie to move to 17-under. However, he closed with eight straight pars to join the playoff.
Third-round leader Richard Johnson struggled to a 1-over 73 in the final round. That left him tied for sixth at 14-under-par 274. He was joined there by Mike Heinen, Peter Tomasulo and Roland Thatcher.