The 23-year-old Levy, playing in his second year on tour, vaulted into the lead with a career-best 10-under 62 in the second round, then held off a late challenge from Fleetwood in the final round to take home his first trophy. He carded a 19-under 269 overall.
Fleetwood, who was trying for his second European Tour title, pulled within one stroke after a birdie the 17th hole, but Levy closed with back-to-back birdies to seal the win.
Fleetwood was second at 15 under and Alvaro Quiros of Spain was third, another two strokes back.
Levy, playing in the group after Fleetwood, looked to be headed for a runaway victory, with a birdie on the 13th from eight feet to extend his lead to five shots.
But then the Frenchman ran into trouble on the par-4 15th. After hitting his approach shot well past the green, he putted from the fringe and sent the ball past the hole off the other side of the green. He chipped back to the green and two-putted for a double bogey, allowing Fleetwood back within two strokes.
"My ball was in the divot, it was a difficult shot with a difficult pin position," he said. "I make double bogey, but I still know I'm playing well."
Fleetwood then tightened the pressure further with a birdie on the 17th to pull another shot back.
Levy responded, however, with a flawless approach shot over a lake on the same hole to set up a 3-foot birdie putt, and another 3-footer for birdie on the 18th.
"I see Tommy make a birdie on the 17th, but I like the pressure, and on the 17th, I'm thinking only to put my ball on the green," he said.
Levy has faltered under pressure before. Last year, he was tied with Ernie Els entering the final round of the BMW International Open but let the title slip away with four bogeys on the back nine. He ended up in third, his previous best result on the tour.
On Sunday, however, the double bogey didn't appear to rattle him. In fact, the smile he's flashed on the course all weekend returned on the very next hole when he just missed a 40-foot birdie putt by inches.
"We aim for wins, but today I didn't really have a chance. I had to play outstanding golf, but Alex has led from Friday, and that's one of the hardest things you can do," Fleetwood said. "What a performance from him."
No. 3-ranked Henrik Stenson, who was bedridden with the flu earlier this week and got no practice on the course, finally put together his first solid round of the tournament, with birdies on seven holes with no bogeys for a 65. The Swede improved to a tie for fifth place but still fell short of the win he needed to overtake Tiger Woods at the top of the world rankings.
"It's really tight and I just need to play better if I want to get to that spot. And I should have to play better than I have done earlier on this year if I want to get to world No. 1, that's for sure," he said. "It really felt like the last month here I'm starting to play better and that's a good sign."
China's top hope, 18-year-old Li Haotong, was looking for his first top-5 finish on the European Tour after starting the day in a tie for seventh. But he never recovered from a quadruple bogey on No. 4 and slumped to equal 50th at 1 under.
PGA champion Jason Dufner opened with a birdie-eagle on his first two holes before slipping back to joint 54th with two double bogeys and a triple bogey on the 17th.