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The 25-year-old Englishwoman finished nine seconds ahead of Australia's Ashleigh Gentle, with Wales' Helen Jenkins seven seconds adrift in third.
Stimpson and Jenkins, 31, will vie for Britain's third Olympic place at next month's World Series event on Australia's Gold Coast.
Non Stanford and Vicky Holland have already secured their places in Rio.
Both missed the race in Abu Dhabi, as did world champion Gwen Jorgensen.
Stimpson said: "I am extremely motivated to make one of the Olympic spots and my winter couldn't have gone any better.
"Me and Helen are great rivals. She is a fantastic athlete and I've got a lot of respect for her. We couldn't have made it harder for the selectors."
Stimpson, who won the first gold medal at the Commonwealth Games in Glasgow in 2014, clawed her way back after a modest 1500m swim to join two-time world champion Jenkins in the leading group for the 40km bike section.
The two Britons led from the front as the challengers were gradually whittled down, before Stimpson used her greater power to pull away in the final kilometre of the 10km run.
Jenkins, who has had a catalogue of injuries in the past two years, said: "Everything is moving in the right direction for our selection race at the Gold Coast.
"It is just a pity Britain could not get four Olympic spots. We will just have to fight it out and do our best."
Britain's selectors have chosen the Gold Coast race as the decider because it most resembles the Olympic course in Rio.
In the men's race, Mario Mola made it back-to-back World Series victories after winning last year's final race in Chicago in September.
Adam Bowden, in 11th, was the highest-placed Briton.
Brothers Alistair and Jonny Brownlee have already qualified for this summer's Olympics and will not compete until later this season.
Britain's selectors will decide who will get the third spot by the Yokohama race on 14 May - the fourth event of the year.
The second of the nine World Series events takes place at the Gold Coast on 9-10 April.

In his closing speech, prosecutor Philip Evans told Woolwich Crown Court the men had given "lies" and "half truths" as evidence during the trial.
Carl Wood, William Lincoln, Jon Harbinson and Hugh Doyle all deny being part in the Â£14m theft.
Four other men have already pleaded guilty to taking part in the raid.
Summing up the case against the accused men, Mr Evans said the robbery had involved a "staggering sum of money" and had been a carefully planned operation by men who knew what they were doing.
He asked the jury to consider whether the "ringleaders" - who had already pleaded guilty - would have trusted those on trial to look after their jewel-laden bags and not take a "peek" inside.
"The men who have pleaded guilty were a group who thrived on acquisitive crime - taking people's money and possessions, greed in reality.
"What they needed were people who wouldn't question that," he said.
Referring to Mr Lincoln's claim that he did not know what was in the bags he helped move, he asked the jury whether they could "believe that for one second?"
"They were never going to let that significant commodity go into the hands of someone they did not trust," he said.
Mr Evans insisted the four men had not told the truth to the court.
"On each of the four occasions that you have heard the defendants give evidence, each of them have told you lies," Mr Evans said.
He added that it did not matter what size role each of the men had played because "if you take part knowingly, you're guilty".
The case continues.
Daniel Jones, 60, of Park Avenue, Enfield; John Collins, 75, of Bletsoe Walk, Islington; Terry Perkins, 67, of Heene Road, Enfield, and Brian Reader, 76, of Dartford Road, Dartford, have all previously pleaded guilty to conspiracy to commit burglary.
Commonwealth champion Jodie Stimpson won the opening race of the 2016 World Triathlon Series in Abu Dhabi.
[NEXT_CONCEPT]
Four men accused of being part of the Hatton Garden raid were trusted to be involved because of their "connections to the ringleaders", a court has heard.