The 38-year-old, chasing his biggest single payday at the $6.5-million event, kept up Friday's momentum as he returned a third-round score of 67 for a 16-under-par total of 200.
He might have held a more comfortable lead had he not bogeyed the 17th at the Gary Player Country Club. "I'm still in a strong position and I've got to go out there tomorrow and play really good golf," he said. "It's a tough field, a lead of three doesn't mean much among these guys."
Donaldson leads from Thomas Bjorn of Denmark and American Ryan Moore, who are 13 under par. Bjorn played one of the best rounds of the day, birdieing the 18th to finish with a 66.
Moore followed a second round 65 with a 67, with five birdies in a bogey-free round. Spaniard Sergio Garcia and Thongchai Jaidee of Thailand both matched Bjorn's 66 to go 11-under, along with world No 3 Henrik Stenson of Sweden, who hit a double bogey at the par-5 ninth to finish with a 69.
Three-time winner Ernie Els, making a record 18th appearance at the tournament, scored a triple bogey early in his round on the way to a 77, for a seven-over total that leaves him tied bottom of the elite 30-man field.
At the Hong Kong Open, Wales' Stuart Manley will take a slender lead into the final round as he bids for a first European Tour title.
Manley carded a third round of 66 to finish 10 under par, one shot ahead of Australia's Wade Ormsby and India's Shiv Kapur.
"Pretty much from the first hole onwards, every iron shot was right down the pin," said Manley, who fired six birdies and two bogeys. "If it had been a good day on the greens it could have been a really low round, but I feel very confident the way I'm playing and I'm really excited about tomorrow."
Despite only securing his card via the qualifying school last month, Manley represented Wales in the World Cup in Melbourne the following week and hit the headlines when he followed a hole-in-one in the third round with an 11 on the next hole.
Thailand's Pornanong Phatlum shot a 66 to claim the Omega Dubai Ladies Masters title in brilliant fashion, edging out world No 3 Stacy Lewis in a final-round duel.
After a promising first three rounds, Vikki Laing slipped back after a disappointing 76, but she still finished joint eighth, along with English teenager Charley Hull, who secured rookie of the year honours on the Ladies European Tour.
Pamela Pretswell's 75 left her joint 46th, while Kylie Walker shot 74 to finish joint 49th.