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Stenson finished at Jumeirah Golf Estates on 12 under par, one shot ahead of Spain's Alejandro Cañizares, who added a 67 to his opening 66.
The 37 year old is looking to become the first man to win The Race to Dubai and FedEx Cup in the same season and is on course to clinch them both in the same imperious fashion.
He went into the Tour Championship in September as one of five players who could claim the FedEx Cup by winning the tournament, and did exactly that.
And this week the Swede is one of three players in similar control of their own destiny, knowing that a win on Sunday would secure overall victory in The Race to Dubai, status as European Number One and a US$1,000,000 bonus.
Justin Rose and Graeme McDowell could still deny Stenson the title with victory in Dubai, with Rose best placed on seven under after a 67.
A win for Ian Poulter would leave Stenson needing to finish second to claim the Harry Vardon trophy, with Poulter alongside Rose on seven under following a 68.
"I have my game plan cemented on this course and it's been working out great the first two days," said Stenson, who carded eight birdies and no bogeys. "It could have been a bit better but there is no point being greedy. I am delighted with the first two days' work.
"I keep track of what's happening with the other players, I'm too curious not to. I saw both Justin and Ian are seven under so they are chasing me as hard as they can.
"They are not going to back down so I better keep my foot and my head down, play another two good rounds and see where that takes me. I am in a great position to have a shot at winning and hopefully I will be there on Sunday afternoon."
Stenson admitted he is battling fatigue from a long season as well as an ongoing wrist injury, but added: "The two days I had off on Monday and Tuesday have helped. I got the club stuck in the ground on the sixth tee and felt it there but thankfully I don't think that made it flare up."
Cañizares has won just once on The European Tour - the Russian Open in 2006 - but boosted his chances of a second title with a brilliant par save on the 18th, where he botched his second shot into a stream before pitching to 12 feet and holing then resulting putt.
“I pull hooked it in the water - it was a terrible shot,” said the 30 year old.
“I gave myself a chance and I really wanted to make that putt, because I haven't dropped a shot in the whole day and I didn't feel like I should have. I made that putt and it felt great.
“I played with Henrik on Sunday, and he's a fun guy to play with, and tomorrow I'm just going to go out there and enjoy it and focus on my game. That's all I can do.”
Rose and Poulter have not given up their pursuit of Stenson, but Rose admitted the 7,600-yard course is "tailor-made" for the likes of Stenson and defending champion Rory McIlroy thanks to their length off the tee.
McIlroy had eagle putts on all four par fives and made one on the 14th in a 67 that left the former World Number One six off the pace on six under.
"I think somewhere around 20 under par will win so I will need a couple of 65s," said McIlroy, who shot back-to-back rounds of 66 to win here 12 months ago. "I finally feel I have got to the stage now when I can contend week in, week out and on the rare times I have got into contention this year I feel like I have played my best golf."
The man McIlroy succeeded as European Number One, Luke Donald, is a shot further back after a 66 that contained six birdies in succession from the second.
Shane Lowry completed his second round in one under par 71 for 29th place.
