The world number three is 12 under par on 132, one shot ahead of first-round leader Alejandro Canizares.
The Spaniard saved par on the 18th with a 10-foot putt after finding the water, while Stenson shrugged off a missed eagle opportunity on the 14th to pick up four shots on the final seven holes.
Stenson went into the European season finale leading the Race to Dubai, formerly known as the European Order of Merit.
The 37-year-old, England's Justin Rose and Northern Ireland's Graeme McDowell would all top the money list should they prevail over 72 holes on the Greg Norman-designed course.
Englishman Ian Poulter and Wales's Jamie Donaldson would do likewise if they win this tournament and Stenson finishes third or lower.
The chasing quartet are struggling to keep up with the nerveless Swede, who did not drop a shot all round and would net a $1-million bonus if he proves to be Europe's top player of 2013.
Rose (67) and Poulter (68) are among a group of players tied for fifth on 137, or seven under, while McDowell (68) and Donaldson (72) are on 140.
(Editing by Clare Fallon)
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