The Swede had an 8-under 64 to reach 12 under after two rounds on Jumeirah's Earth Course.
Stenson also leads the Race to Dubai standings. The points champion will receive $1 million from a $3.75 million bonus pool that counts on the final money list. In September, Stenson won the PGA Tour's season-ending Tour Championship in Atlanta to take the FedEx Cup title and $10 million bonus.
Spain's Alejandro Canizares was second after a 67.
Stenson is trying to become the second Swede to top the money list, following Robert Karlsson in 2008.
Stenson had a five-stroke advantage over England's Justin Rose, second in the points standings. Graeme McDowell, third in the points race, was eight strokes behind Stenson.
"They are chasing me as good as they can, and I know neither one of the guys are going to back down," Stenson said. "So it is better I keep my foot down and my head down and try and keep the momentum going."
Stenson also won the Deutsche Bank Championship outside Boston en route to the FedEx Cup title.
"The key for me this summer was that I have been up so many times," Stenson said. "When I needed the putts to drop they did in Boston, and when I played really well to win in Atlanta (U.S. Tour Championship)."
Rose, the U.S. Open champion, says it is becoming increasingly difficult to catch Stenson.
"I thought that 5-under par would be good enough for me to just stay in the tournament, which I am happy about," Rose said. "But then this golf course seems really tailor-made for Henrik. He just seems to be able to take advantage of all the par-5s, and he's playing really, really well. It will be tough to catch him."
Defending champion Rory McIlroy was tied for ninth at 6 under after a 67.
"It's nice to know going into the weekend you still have a chance to win the golf tournament, and that's the stage I've been trying to get to for the last few months," he said. "I finally feel like I've got to the stage now where I can contend week-in, week-out."