The Frenchman held a narrow one-shot lead in the closing stages on Sunday afternoon before holing out from a bunker at the 17th for a birdie to stretch his advantage to two.
And even though he ran into trouble at the 18th, a bogey there was enough to secure a one-shot win as he closed with a 66 to finish the tournament on 18 under par.
Min Woo Lee needed an eagle at the last to force a play-off and came agonisingly close to getting it as his approach finished two feet from the cup.
The Australian finished in a tie for second alongside Sebastian Söderberg on 17 under, while 51-year-old Pádraig Harrington was another shot back in fourth place on a record-breaking day at Yas Links Abu Dhabi.
Early starter Sami Välimäki shot a course-record 62 with a bogey-free round that consisted of an eagle and eight birdies.
We also saw two players make a hole-in-one, with Dan Bradbury winning a new Genesis G70 Shooting Brake 2.0 Sport at the 17th and Tyrrell Hatton taking advantage of the par-three 13th with a pitching wedge.
Perez got off to a stunning start on day four, reeling off six birdies in the first 11 holes to reach the summit before dropping his first shot of the day at the 14th.
That opened the door for the chasing pack, with Lee joining him at the top of the leaderboard, but Perez bounced back with a 13-foot birdie at the 15th before pitching his tricky bunker shot at the 17th on to the green and spinning it in for a miracle birdie.
He found a bunker off the 18th tee before getting into more trouble but managed to escape with a bogey there to win by one for his third DP World Tour title.
In his post-round interview, Perez said: "I got off to a good start, and I was just focusing on me and trying to do the best I can because I knew you can't control what everybody else is doing, and I was just trying to plod along.
"But Seb (Söderberg) played fantastic and was right there and never gave me an opening. I'm delighted to finish on top. It was a crazy finish, but I feel like I'm used to that now. Hopefully I can make it a little easier for the next one."
Speaking about his phenomenal bunker shot at the 17th, Perez added: "It wasn't actually as difficult as a bunker shot because it was downhill to the hole, flat at the hole and into the wind.
"So I was basically trying to fly it all the way to the hole, and if I hit it a little bit heavy it was maybe going to release.
"But in the back of my mind, I'm just thinking Seb is going to make a two and it's three and a half from where I am, pretty much.
"Hopefully I make a three and maybe I make a four and then we are tied with the last hole to go. It came up maybe a little skinny, I'm not going to lie, and spun back and the fortune of the ball going in which is probably the greatest shot I've ever hit."
The victory means Perez tops the Race to Dubai Rankings in Partnership with Rolex, while it gives his Ryder Cup chances a huge boost.
He said: "It's a great year ahead. There's a lot of big things coming up. I've had a really good off-season. I've worked really hard."