Stenson shot a final round 2-under 70 to win by two strokes with an overall 16-under 272 on the Earth Course at Jumeirah Golf Estates.
Three of Stenson's teammates on Europe's victorious Ryder Cup team — top-ranked Rory McIlroy (68), Victor Dubuisson (68) and Justin Rose (69) — shared second on 14-under 274.
It was the first time Stenson has successfully defended a title and guaranteed that the 38-year-old Swede finishes second to McIlroy in the European Tour Race to Dubai.
"It was such a great place for me to win here last year, so to come back and successfully defend is very pleasing," Stenson said. "I'll be back and try to make it three wins in a row next year."
Rose picked off three birdies in succession from the 14th while Dubuisson birdied the last.
Stenson went to 15 under when he birdied the 17th. While he was in the rough at the last, he found the fairway with his second shot before landing his third pin-high right and sealed the fate of his three Gleneagles colleagues by holing the 15-foot birdie putt.
McIlroy had briefly threatened with birdies on the 14th and 15th.
"I never expected 14-under par would have the remotest chance of winning this golf tournament," said McIlroy. "It just seemed like no one really took the tournament by the scruff of the neck and went with it. But then I didn't play well enough to win this week."
Rafa Cabrera-Bello (75) was leading with three holes to play but the Spaniard tumbled down the board with back-to-back double bogeys at Nos. 16 and 17 to finish tied for ninth with an overall 277.
Cabrera-Bello was looking for a second victory in Dubai after capturing the 2012 Dubai Desert Classic.