Former U.S. Open Champion McDowell, the highest-ranked player in the field, battled back from two holes down after four and one at halfway to secure his eighth European Tour title.
"I'm very excited because it's a massive event and it was hugely disappointing to lose the final last year," said McDowell, who was beaten by Belgium's Nicolas Colsaerts in 2012. "This was a fantastic week for me."
"It's a magnificent golf course at the Thracian Cliffs with a great crowd and I hope we gave the Bulgarians a little taste of what we do."
Thongchai, a five-time European Tour winner, holed a 25 footer at the second to go one up with a birdie and then doubled his lead at the long fourth by converting from five feet after McDowell missed a 10-foot birdie attempt.
McDowell, who secured his final berth with a 3 & 2 win over South Arica's Branden Grace earlier on Sunday while Thongchai beat South Africa's Thomas Aiken 3 & 2, cut the deficit when he birdied the short seventh from six feet and levelled with a birdie at the 12th.
He took the lead for the first time by winning the 14th with a par after Thongchai drove into a bush and had to play out sideways, went two up after taking the 15th after a brilliant approach to five feet and closed out the match with a par on 17.
The $3.85 million tournament was staged at the the picturesque Black Sea resort of Thracian Cliffs near Kavarna as Bulgaria hosted a tour event for the first time after the competition was moved from Spain.