Stenson had four birdies on each side, moving ahead of Alejandro Canizares for the tournament lead. Stenson is at 12-under 132 after 36 holes, one stroke up on Canizares, who led after the first round.
Stenson entered the final event on the 2013 European Tour calendar in first place in the Race for Dubai, which determines the European No. 1 golfer. The tournament has a total purse of $8 million and a bonus pool of $3.75 million for the Race to Dubai.
Stenson is five strokes ahead of Justin Rose, who is the closest player to challenge him for the Race to Dubai title.
Victor Dubuisson, who picked up his first European Tour win Sunday in Turkey, had a second-round 66 and is tied with Marcus Fraser for third at 8-under 136. Fraser turned in a 3-under 69.
Jonas Blixt shot 65 and pulled into a tie for fifth with Kiradech Aphibarnrat (70 Friday), Ian Poulter (68) and Rose (67) at 7-under 137.
Defending champion Roy McIlroy shot 67 and moved up to a tie for ninth at 6-under.
Stenson played the four pars 5s at the Jumeirah Golf Estates in 3-under and closed each side with a birdie in taking the lead.
Canizares was 3-under through seven holes and added birdies at 13 and 14. He closed with four straight pars, including a save after his second shot at the par-5 18th ended up in a water hazard and finished with a 67.