The 45-year-old shot a three-under-par 69 in the final round for a winning total of 16-under-par 272 at the Kota Permai Golf and Country Club.
India's rising star Gaganjeet Bhullar was second in the $395,000 event, with Vietnam's Michael Tran, Bangladesh's Siddikur and Spain's Javi Colomo tied for third another shot behind.
"I'm very glad to win this tournament," said Thaworn, who pocketed $60,900 for his record triumph, according to an Asian Tour press release.
"When I played in the practice round, I thought I would have a disadvantage on the par fives but I holed a few birdies and my confidence started to build.
"The first time I joined the Asian Tour, I couldn't make the cut. I never thought I would come this far. After I won my first title (1996 Sabah Masters in Malaysia), I thought I could win more and I kept practising more and more to make myself better."
Bhullar, 24, said Thaworn who held a three-shot lead overnight, was too far ahead to catch.
"He's an experienced guy as he knows how to close the deal. Congratulations to him," he said.
Tran, 22, Vietnam's only player on the Asian Tour, has thought about quitting the game after a lack of success.
"This should give me some hope to get into the events later like the Thailand Golf Championship and Iskandar Johor Open. If I can get my card by finishing in the top-60 (of the Order of Merit), it will change my decision," he said.
Final scores at the Worldwide Holdings Selangor Masters 2012 being played at the par 72, 6977 yard Kota Permai GCC course:
272 - Thaworn Wiratchant (THA) 66-69-68-69
275 - Gaganjeet Bhullar (IND) 68-71-70-66
276 - Siddikur (BAN) 73-71-66-66, Javi Colomo (ESP) 68-69-72-67, Michael Tran (VNM) 67-68-73-68
278 - Jason Knutzon (USA) 72-68-70-68, Jesper Kennegard (SWE) 70-69-67-72