Jaidee began the day with a two-shot lead over McIlroy and Wang Jeunghun and never looked in danger of being caught thanks to a closing 68 at Le Golf National, venue for the 2018 Ryder Cup.
The 46-year-old former paratrooper carded four birdies and a solitary bogey on the 18th, his first dropped shot since the 13th hole of his second round, to claim a fourth win - all of them in Europe after four in Asia - since turning 40.
At 11 under par, Jaidee finished four shots clear of Italy’s Francesco Molinari, whose 66 was the lowest round of the day, with McIlroy another stroke back after a 71 containing one birdie, one bogey and 16 pars.
“It’s my biggest win ever,” said Jaidee, who dedicated the win to his son on his birthday.
“I played great this week, no complaints at all. I had Rory two shots behind me but I tried to play my own game, hit a lot of fairways and greens and I knew this week I was putting well.”
Jaidee quickly extended his overnight lead to five shots thanks to birdies on the third and sixth and although former champion Martin Kaymer and England’s Andy Sullivan briefly closed to within three, they soon faltered as Jaidee continued to play flawless golf.
Birdies on the 11th and 15th effectively sealed victory for Jaidee and lifted him from 57th in the world rankings to inside the top 40 just a fortnight before the Open Championship at Troon.
“I said to family I wanted to get back into the top 50 so this is going to be very good for me,” Jaidee added. “The Open is my favourite tournament so I am very excited to see what I can do in two weeks.”
McIlroy, who has been working hard to eradicate some “bad habits” from his game, never threatened to claim a second win of the season after a bogey on the third and took until the 14th to register his only birdie of the day.
“It’s been a good week to see where I’m at with my game,” McIlroy said: “There were signs it was really good and heading in the right direction and today again some signs it was good but a few swings on the back nine I need to work on.
“The way I’ve felt out there and to finish third on my own, it’s been a decent week in that regard.
“I’ve got 10 days until the Open starts. I’m going to be working every day to try and get better and will play a bit of links golf to work on the shots I need for Troon as well. Even though this week it didn’t feel that good I’m obviously doing some things right.”
McIlroy, who lifted the Claret Jug at Hoylake in 2014 but was unable to defend the title last year after suffering an ankle injury playing football, added: “I’ve not played Troon but am going over for a couple of days to work out what I need to do.
“It was really disappointing, especially at St Andrews last year, not to be able to defend.
“The last time I played the Open I won it so good memories and hopefully I can play similar to the way I did in Liverpool and give myself a chance.”
Spain’s Rafael Cabrera-Bello boosted his chances of a Ryder Cup debut in September after a closing 67 left him in outright fourth, but Sullivan’s hopes of making the European team were dented by a costly finish.
Sullivan had looked set to claim second place when he carded four birdies in five holes from the 12th to reach eight under, only to bogey the 17th and run up a triple-bogey seven on the last to drop into a tie for fifth with Kaymer and South Africa’s Brandon Stone.
Stone, Sweden’s Alex Noren, England’s Callum Shinkwin and South Africa’s Richard Sterne secured the four places in the Open on offer to players, not otherwise exempt, who finished in the top 12.