The 23-year-old never actually surrendered the lead on Sunday but saw his six-shot overnight advantage cut to a single stroke by Fitzpatrick during a thrilling final-round battle in the pouring rain at Hong Kong Golf Club.
Five-time European Tour winner Fitzpatrick had fired seven birdies in his first 16 holes to pile the pressure on Rai but his challenge faltered when he carded his first bogey of the day at the 17th to give his compatriot a two-shot cushion with one hole remaining.
And despite carding a bogey at the last, Rai signed for a closing 69 to finish on 17 under par and open the 2019 Race to Dubai campaign with a stunning wire-to-wire victory in just his 46th European Tour appearance.
Fitzpatrick’s sensational 64 saw him finish alone in second on 16 under, with Challenge Tour graduate Victor Perez and Australian Jason Scrivener five shots further back in a tie for third place.
Scot David Drysdale was on his own in fifth after Sunday’s 66, while India’s Shubhankar Sharma and Spanish pair Sergio Garcia and Rafa Cabrera Bello were another stroke back in a share of sixth.
Aaron Rai said afterwards: “It’s incredible. It definitely hasn’t sunk in just yet. I’ll probably need a few days for that to happen.
“It’s incredible to win on any Tour, let alone The European Tour and let alone the Hong Kong Open. It’s an incredible course, incredible event, very well supported. The crowds have been amazing. I’m just very grateful.
“Matt played incredibly all day. It was tough but again, I really just tried to play the course as much as possible, rather than Matt, or anyone else who was playing well today.
“I luckily managed to do that for most of the way around. It’s tough considering the situation but I’m very pleased.”
“It felt a little bit different today. It’s nice having wins in the past which help you kind of in what to expect in a sense, but it did feel a little bit different today in terms of just how big it is and the attention of people.
“Also playing with two real world class players in Tommy Fleetwood and Matt Fitzpatrick. I’ll have to re-evaluate myself before I can give you a good answer of what I learned, but I think just staying even more patient, really getting further into your own game, compared to just being aware of what the other guys are doing. I think the more you play against world class players like that, you kind of expect that they will never make it easy.”