Ireland’s triple major winner came through a stuttering start to the final round and then a thrilling 18th hole to card a winning total of 16-under-par 268.
The victory is Harrington’s first at a full field tournament since he lifted the Johor Open title in 2010.
It was far from plain sailing for the world number 385, who had entered the final day with a four-shot lead before a poor start allowed Thanyakon to go two shots clear after nine holes.
A two-hour rain break seemed to stall the Thai’s momentum, however, and Harrington fought back to restore parity with his rival heading to the 18th.
The Irishman skewed his tee shot to the edge of a hazard but Khrongpha failed to capitalise, finding the water with his second and registering a double-bogey six.
Harrington recovered his composure, sinking a 15-foot putt to make par and secure a dramatic victory.
Meanwhile, Danny Willett picked up the second European Tour title of his career after carding a final-round six-under-par 66 to convincingly win the Nedbank Golf challenge in Sun City, South Africa.
The Englishman holed six birdies yesterday to finish 18 under for the tournament and seal a four-shot victory, beating fellow countrymen Ross Fisher and Luke Donald to the prize. It was a frustrating final round for Donald, who came into the final day leading by a shot on 13 under, but could only close with a one-over 73.
He ended up finishing two shots behind Fisher, who registered seven birdies and three bogeys in a final-round 68.
Marcel Siem finished three shots further back on nine under after shooting a 68, while Thailand’s Kiradech Aphibarnrat was fifth on seven under.