The Thai ace began the final round of the $1.25 million co-sanctioned tournament with a stroke advantage and moved ahead by as many as four shots with birdies on four of the first seven holes at New Kuta Golf Club.
Bogeys on the eighth and 14th saw his lead trimmed to one but a birdie on the 16th gave him a cushion to take into the closing holes as he finished at 12-under-par 276 ' two strokes ahead of Swedens Alexander Noren and the English pair of Steve Webster and Simon Dyson.
Noren shot a closing 70, Webster fired a bogey-free 68 while Dyson was left to rue a double-bogey on the 14th in his closing 69.
Rafael Cabrera Bello of Spain carded the days best round of 65 to join Richard Bland (70) in a tie for fifth at 9-under with Jyoti Randhawa of India (70) and the English pair of Simon Griffiths (71) and Simon Khan (68) another shot back at 8-under.
Thongchai continued a trend that has seen the third-round leader or co-leader win every edition of the Indonesia Open since it was revived as a joint-sanctioned event by the European and Asian Tours in 2005.
Nursing a narrow lead at the start of the final round, he parred his first two holes before sinking consecutive birdies on the next three including a chip-in on the fifth.
The 39-year-old narrowly missed out on a fourth in a row when his long putt lipped out on the sixth, but he holed his birdie attempt from the fringe on the seventh to improve to 13 under.
That briefly gave him a four-shot advantage but he gave one back with a bogey on the par-3 eighth after putting his tee shot into the bunker and blasting well past the pin from a dreadful lie in the sand.
His lead appeared fragile at times on the back nine and he found himself just one ahead of Webster when he bogeyed the 14th after putting his approach shot into rough and failing to get up and down.
With Webster failing to capitalize on birdie opportunities on his closing holes, the Thai player managed to stretch his advantage once again with a birdie on the 16th.
He nearly found trouble when he missed his approach shot on the final hole, but he holed a testing par putt from eight feet to close out his third win on the European Tour and 11th on the Asian Tour.