The Northern Irish former world number one shot a six-under-par final round of 66 to finish on 21 under, one clear of England's Andy Sullivan.
Victory means 26-year-old McIlroy retains his Race to Dubai title, the third time he has won it in four years.
England's Danny Willett finished tied for fourth in Dubai, and second to McIlroy in the season-long standings.
McIlroy said: "It's the best way to finish 2015 and I can't wait for next year."
The four-time major winner carded eight birdies in Sunday's first 15 holes to open a two-shot lead over Sullivan, only to find the water with his tee shot on the 17th.
But McIlroy holed a 30ft putt to salvage a bogey and stay a shot ahead of overnight leader Sullivan.
He maintained that advantage down the last to win his fourth title of the year and first since May.
McIlroy missed three tournaments this summer, including the defence of his Open title at St Andrews, because of an ankle injury sustained while playing football.
That meant he needed an exemption to compete in the European Tour's season finale, having not played in enough events.
McIlroy said 29-year-old Sullivan, who finished eighth in the Race to Dubai, would be an "asset" for Europe's Ryder Cup team.
"Luckily I came out on top but he's a fantastic player," said McIlroy, who added a £822,828 bonus for winning the Race to Dubai to the £934,599 he banked for his World Tour Championship victory.
"He kept holing putt after putt and I just kept chipping away, and thankfully I holed a few good ones of my own coming down the stretch."
Rory McIlroy won the World Tour Championship in Dubai to finish the season as Europe's number one golfer.