Another birdie on the fourth handed him a six-shot lead and while Bourdy closed the gap, a closing gain put Hatton in further control.
Ross Fisher broke the scoring record at the Old Course with an 11-under, 61.
Yet it was Hatton who commanded the field, holding a five shot lead heading in to the final day of the tournament and ending the day three shots clear of Fisher to win his second European Tour title.
The course was setup for the Dunhill Links' Pro-Am format without the treacherous pin positions and rough, and with its October date the fairways and greens are never going to be as firm and fast as July for the Open Championship.
It's safe to say Sunday offered the former for Tyrrell Hatton. Maybe that's just a bit more pressure on myself but I'm so happy that I managed to defend it and what a great week again.
"I played baseball for two years, and even went to Japan. We've just had good fun, I think that is what this tournament is about". It felt like it was a lot harder today than it was previous year.
He seems to have come out of the wilderness and that's good news for golf as he's a great character and a very flamboyant player. I just saw the lines and was hitting good putts and they were going in and I didn't want it to end.
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"When you get St. Andrews on a day like this, it's definitely scoreable, but you still have to hit the shots", he said.
Countryman Grégory Bourdy, England's Robert Rock and Scot Marc Warren were then ten shots behind the victor, with English trio Luke Donald, Oliver Fisher and Eddie Pepperell, Ireland's Paul Dunne and Frenchman Alexander Levy at 13 under.
McIlroy will now take three months off before returning to competition in mid-January.
Playing his first event since becoming a father for the first time last week, Fleetwood birdied six of the last eight holes to complete a bogey-free round and beat the course record by a shot.
Golfweek's Geoff Shackelford addressed Player's comments on Golf Channel's Morning Drive on Monday morning, and said he thinks that we could see equipment being regulated by governing bodies at some point.
Another man who also made significant strides up the season rankings is Robert Rock.
"I feel I'm a much better player than I was in 2011 and 2012, when I was able to win a couple of majors".