At 10-under-par 134, Stenson holds the lead after two rounds for only the second time on the European Tour. He is one shot better than Ricardo Gonzalez of Argentina, who shot a 3-under 69 in his second round.
Stenson and Gonzalez shared the first round lead after firing matching 66s at Doha Golf Club on Thursday.
England's Nick Dougherty posted a 5-under 67 and is tied for third place at minus-eight after two bogey-free rounds. He is joined by countryman Richard Finch, who has carded two 68s.
Thailand's Prayad Marksaeng shot a 67 and is alone in fifth place at 7-under, while Niclas Fasth of Sweden is one stroke further back in sixth after a 70.
Defending champion Ernie Els equaled his first round score of 71 and is tied for 28th place at minus-two.
By making the cut, Els matched Bernhard Langer's record of consecutive cuts made on the European Tour at 69. The South African has made every cut since the 2000 Johnnie Walker Classic.
World No. 2 Vijay Singh also shot a 71, but is way back in a tie for 45th place at even par. Singh shared eighth place last week at the inaugural Abu Dhabi Golf Championship on the European Tour.
Danny Denison, the only amateur in the field, stumbled to a six-over 78 after making a splash Thursday by shooting a 5-under 67. Denison, who was tied for second place overnight, is competing in his first professional tournament.
Stenson played in an early group and began his round on the 10th tee. He carded two birdies -- at the 13th and 18th, both for the second straight round -- and a bogey to make the turn at 7-under.
Three straight pars were followed by three birdies during a five-hole stretch, as Stenson moved clear of his early competition to grab the clubhouse lead.
Stenson wasn't pleased with his putting on the day, but in many cases, like at the par-4 sixth where his approach landed within two feet for birdie, he didn't need a good flat stick.
'It was a bit of a struggle, but a 68 is a 68 no matter how it looks,' Stenson said. 'I was striking the ball better yesterday.'
The only other time Stenson led after two rounds on the European Tour was at the 2001 Benson & Hedges International, which he won. Stenson was second last week in Abu Dhabi, one stroke behind winner Chris DiMarco.
'I must keep working on my putting...and if I can set up a notch then I think I can have a good weekend,' the Swede said.