The 47-year-old, who started the day a stroke back from Bangladesh's Siddikur Rahman, shot a four-under-par 67 that included eagles on the eighth and the final hole, to move clear of the chasing pack with a 14-under total of 270.
Compatriot Arnond Vongvanij finished second while Japan's Daisuke Kataoka was third, five shots adrift.
Prayad started the day with a bogey on the first hole at the Santiburi Samui Country Club, where he had finished in the top-three on three occasions since 2009.
He dropped another shot on the seventh after birdies on the fourth and sixth and the eagle on the eighth calmed his nerves.
He made nine consecutive pars after that and signed off in style amid loud cheers from the home crowd.
"When Arnond bogeyed the 12th, I had a feeling that this would be my week. I've been struggling with injuries for so long and I finally got my game together this year," Prayad told the Asian Tour website (www.asiantour.com).
"I've come so close to winning here but couldn't finish the job previously. So obviously this win really means a lot to me."
Siddikur finished in a tie for eighth spot after a dismal six-over-par final round of 77.