The world number four, who topped the Race to Dubai and FedEx Cup standings courtesy of victory at the European Tour's season-ending event 12 months ago, is well placed to defend a title for the first time in his career after progressing to 10 under at Jumeirah Golf Estates.
Stenson is two clear of Danny Willett, Richie Ramsay and first-round leader Rory McIlroy, this year's Race to Dubai winner, after improving on his opening 68 by two shots.
Three of the Swede's seven birdies on Friday came in the final six holes, yet Stenson revealed fatigue had started to set in by that stage.
"There's still a lot of golf to play and I'm really happy with how I closed this round," the Swede is quoted as saying by the European Tour's official website.
"Around the 12th hole I felt like I was running out of steam. It was difficult mentally from there on. I had to really focus hard and drag myself over the finish line.
"It's hot and sticky and even though I'm drinking well and getting plenty of energy, I just felt like I hit the wall on 12.
"If it's one or two holes left, you normally feel like, 'okay, I can hang on'. But it was a bit of an uphill [battle] from there. I managed to finish in good style anyway so I'm pleased with that."
McIlroy could only muster a 70 in his second round and is aware he faces a challenge to overhaul the man who triumphed with a score of 25 under in Dubai last year.
"I'm in a good position and there is a lot of golf left," said the world number one.
"I've definitely been in worse positions after two rounds and still won.
"Henrik's very comfortable on this golf course obviously. I can't let him get too far ahead tomorrow [Saturday].
"I have to get off to a fast start and try and put a bit of pressure on him. Hopefully I can do that."