It marks a successful start to the Spanish superstar's career rebuild following the demise of LIV Golf.
Rahm shot five-under 67 and was 23-under par at Yas Links, two strokes clear of Hatton (68) and four ahead of McIlroy (69) in the first of the two season-ending playoff tournaments in the United Arab Emirates.
This was Rahm's first event in seven weeks, during which time his wife gave birth to their fourth child and he set about finalising a departure from the LIV tour.
Meanwhile, Australia's Adam Scott, who didn't drop a shot over the first three rounds and was just three off the lead in fifth place overnight, finally did so three times to finish joint-ninth after a final-round, one-over 74.
The 46-year-old former Masters champion was gunning to become the first player since Swede Jesper Parnevik won the 1995 Scandinavian Masters to go through 72 holes in flawless fashion, without recording a single bogey.
But bogeys on hole seven and nine and the par five 14th, saw him him eventually finish tied with Englishmen Nathan Kimsey and Matthew Jordan, Germany's Freddy Schott and Frenchman Frederic Lacroix on 14-under 274 for the tournament.
Rahm is sure to be heading back to the established tours for next season and acknowledged Sunday's win was a new stage in his life.
"After everything that's gone on," Rahm said, "and some poor play and some battles mentally with a lot of noise, to come back out after a bit of rest and being with the family, it's quite special."
His last victory on the European tour's regular circuit was the World Tour Championship in November 2022, which was followed by a green jacket at the Masters a few months later and then the world No. 1 ranking before a controversial move to LIV.
At one stage early in the back nine, Rahm, McIlroy, Hatton and Francesco Laporta were tied for the lead on 20 under, only for Rahm to pull away with three birdies in five-holes from the 11.
McIlroy's Sunday charge, which started with a birdie and an eagle on his first two holes of the day, slowed with a bogey at No. 15, while Laporta fell out of contention with a triple-bogey at par-3 13th.
The Italian wound up shooting 72 and finished alone in fourth, six strokes behind Rahm.
Hatton, meanwhile couldn't make enough birdies to reel in Rahm, who walked down the par-5 18th with a two-shot lead and played it safe to make par.
McIlroy's disappointment at failing to win will have been slightly tempered by his surge in the season-long Race to Dubai standings.
With his third-place finish, the world No. 2 moved above Patrick Reed and into second place, behind only Eugenio Chacarra with one event left, next week's World Tour Championship in Dubai.
Spaniard Chacarra, 26, in his first full season on the tour, finished tied for 22nd this week and Reed tied for 43rd in the 70-man field.
Northern Irishman McIlroy is almost 534 points behind Chacarra, with 2,000 on offer for the winner next week and is looking to join Scotsman Colin Montgomerie on a record eight Race to Dubai titles.
"I would have loved to have won the tournament, but enough positive signs to feel good going into next week." McIlroy said.
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