The 39-year-old, a resident of Dubai, was tied for the lead at 22-under par with Tyrrell Hatton, who also birdied his last two holes of the 9 million dollar (8.4 million euro) tournament.
Waring delivered the hammer blow on the chasing pack with a 41-feet birdie putt on the par-3 17th hole, and then hit a brilliant three-wood second shot to set up a birdie on the last.
At 24-under overall, Waring finished two shots ahead of Hatton (64). World No.3 Rory McIlroy (64) was in a three-way tie for third place at 21-under alongside Matt Wallace (63) and Thorbjoern Olesen (66).
McIlroy fell one shot shy of wrapping up the Order of Merit crown ahead of the season-ending DP World Tour Championship next week.
A second-place tie would have made his lead insurmountable over the second-placed Thriston Lawrence of South Africa.
Waring, who shot a course-record 61 on Friday en route to a new DP World Tour 36-hole scoring record of 19-under par, began the day one ahead of Denmark's Niklas Norgaard, Moller and birdied the first two holes to get off to a good start.
Even as others behind him made plenty of birdies, the world No. 229 kept making steady pars and raced ahead on the closing stretch.
He said the birdie putt on the 17th was pivotal.
"That was massive," Waring said, adding he discussed the line with caddie Alex Evans.
"We really, really fancied it as soon as it left the blade, I knew it was dead middle. I don't want to sound cocky, but it was so pure," said Waring.
It was Waring's second win on the DP World Tour, coming nearly six years and three months after the 2018 Nordea Masters.
He pocketed 1.53m dollars million and should rise to 101 in the world rankings on Monday.
"It's my second win. I've been knocking on the door a few times. I had a few seconds. To get over the line again is fantastic, and to control it the way I have, especially today, after I thought I might have let it slip yesterday."
A bonus for Waring would be a possible card on the PGA Tour. The top-10 players at the end of the DSP World Tour Championship, who are not already members of the US Tour, will secure their playing privileges for 2025. Waring improved to fifth place in the Order of Merit after the win.
McIlroy, who made a triple bogey on the par-3 17th on Friday and a double bogey on the par-5 18th in the third round, said: "I think the two finishes on Friday and Saturday left me with a bit of work to do.
"I do feel in a good position. I saw Thriston making a charge today, and I was keeping one eye on the leaderboard and looking at what he was doing," said McIlroy. "I wanted to birdie the last even though I knew that birdie wasn't going to win the tournament this week."
"It gives me that little extra cushion going into next week."
The DP World Tour moves 120 kilometres to the neighbouring emirate of Dubai next week. Only the top-50 players from the Race to Dubai qualify for the season-ending championship.
