The former Ryder Cup player, a seven-times winner on the European Tour, followed up his eight-under 64 on Friday with another low-scoring display as a 66 gave him a 16-under aggregate of 200.
American Phil Mickelson, the highest-ranked player in the event, was in a group of four players sharing second place.
The world number eight was slow to get going on Saturday but six birdies in the last 11 holes secured a 66 and put him alongside South African Branden Grace (66), Dane Joachim Hansen (69) and Briton John Parry (66) on 202.
"I feel like the game has been sharp and I finally got the score out of it over the last 11 holes," said Mickelson.
The 43-year-old has tended to struggle on links courses this side of the Atlantic and a win would provide a huge confidence boost ahead of next week's British Open at Muirfield.
"It would be a great step in the right direction in my desire to try to capture a first British Open," he said.
Stenson, who won the South African Open title in November, was happy with his performance on Saturday.
"It was probably as good as I've felt all year tee to green," he said. "That's very promising and I'm pleased with that.
"I'm going to do my best tomorrow. It's always a challenge to close out golf tournaments and to win."
Britain's Gareth Maybin stormed up the leaderboard with the best round of the day.
His eight-under 64 included an eagle at the par-five sixth hole, eight birdies and two bogeys.
Maybin, Frenchman Raphael Jacquelin (65) and American Peter Uihlein (70) are on 203.
Overnight leader Chris Doak of Scotland struggled to a 73 for 205.
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- Branden Grace