Khongwatmai, who turns 16 in May, showed little signs of pressure when he fired two eagles for a six-under-par 66 and a 20-under-par 268 total at the Kelab Rahman Putra Malaysia.
The teen defeated local hope Danny Chia and Shane Smith of the United States, who closed with a 70 and 64 respectively, to settle for tied second at the RM200,000 (approximately US$55,400) ADT event.
Sutijet Kooratanapisan (69) of Thailand finished a further shot back on 273 while Quincy Quek of Singapore, the halfway stage leader, finished fifth following a 69 for a 274 total.
Phachara, who held the share of the overnight lead with Chia, got off to a flying start when he eagled the third hole from 10-feet before making the turn in 34.
He pulled clear from the chasing pack with a huge 25-footer eagle on hole 10 before ending his round on a flourish with birdies on holes 15 and 18.
The victory is a huge boost in his fledging career. He made headlines when he won the 2013 Hua Hin Open on home soil at the age of 14 before turning professional in August last year.
He also earned an Asian Tour card at Qualifying earlier this year after winning his first professional title in Thailand.
"I’m very happy with this win," smiled Phachara. "I couldn’t have asked for a better way to win a tournament because my game was very good. I was a bit nervous but it helps when you have two eagles in your round! My short game really helped me this week."
Phachara’s win earned him US$9,436 and six valuable Official World Golf Ranking (OWGR) points.
The ADT will reward the top-five finishers on the Order of Merit at the end of this season with Asian Tour cards for 2016.
With the Olympic Games looming in 2016 where golf will be reintroduced as a medal sport, players in the region could earn their spots in Rio de Janeiro by earning Official World Golf Ranking points through the Asian Tour and ADT.
For more information on the ADT, please visit www.asiandevelopmenttour.com
Leading fourth round scores:
268 - Phachara KHONGWATMAI (THA) 71 66 65 66
272 - Shane SMITH (USA) 68 69 71 64, Danny CHIA (MAS) 68 68 66 70
273 - Sutijet KOORATANAPISAN (THA) 68 69 67 69
274 - Quincy QUEK (SIN) 67 67 71 69
276 - Brett MUNSON (USA) 68 69 66 73
277 - Thammanoon SRIROJ (THA) 68 73 68 68
279 - Ervin CHANG (A) (MAS) 70 69 72 68
280 - Lindsay RENOLDS (CAN) 71 69 72 68, Casey O'TOOLE (USA) 69 73 69 69, KHOR Kheng Hwai (MAS) 70 67 72 71, Abel TAM (MAS) 72 67 69 72
281 - Pavit TANGKAMOLPRASERT (THA) 71 71 69 70