Knutzon fired a closing four-under-par 67 at Macau Golf and Country Club to seal his maiden Asian Tour triumph over Thaworn, who finished with a superb round of 65.
Overnight leader Amandeep Johl of India and Taiwan's Lu Wen-teh finished joint third, with Harrington and last year's runner-up Scott Barr of Australia sharing fifth.
The final round was a thriller, with Johl, who had led since the opening round, maintaining his grip through the front nine. When he made the turn, he led by two strokes but an errant tee shot on 10 which landed in thick bushes led to a double bogey six.
Barr, who lost in a play-off to Colin Montgomerie last year, grabbed the lead on the 12th hole but double bogeyed the 13th to fall out of contention. It was a similar story with Harrington, the Macau Open's top draw. He closed the gap with three birdies in his opening six holes but stumbled with a costly triple bogey on the eighth.
Meanwhile hopes for Ireland's first European Challenge Tour victory of the season ended in disappointment in Italy yesterday as the Irish trio of Stephen Browne, Michael Hoey and Colm Moriarty completed their fourth and final rounds of the Tessali-Metaponto Open di Puglia e Basilicata.
Browne, Hoey and Moriarty finished the tournament with respective scores of two, three and four over par, with Leif Westerberg of Sweden taking the title with an aggregate total of 11 under.
Westerberg, who was one over for the final round after 11 holes, produced an amazing comeback picking up five birdies in his last six holes to overcome overnight leaders Craig Williams and Oliver Wilson.
The Irishmen on the Challenge Tour, meanwhile, have a three week break before their next tournament, the Nykredit Danish Open, which will herald the beginning of a hectic summer period that will see 11 tournaments played over June, July and August.
Those three months will be crucial in the race for the top 15 places on the Challenge Tour Rankings, where Belfast 25-year-old Hoey is currently the best placed Irishman in 15th position, having accrued €16,338 in prize money so far this season.
England's Bob Cameron won the Open de France Seniors at the Omaha Beach Club in Normandy yesterday.