Lee, who led a stellar field in last month's Abu Dhabi Championship with one round to play but had to settle for a share of 10th place, added a four-under 67 to his opening 65 for an 11-under 132 and sits in a share of the halfway lead with Italian Ryder Cup player Edoardo Molinari.
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Lee, aiming to become the second Scot in a row to win on the tour after Stephen Gallacher's triumph in Dubai last weekend, made an early raid with four birdies on his opening eight holes. He could only muster a level-par inward half, however, as he finished in a tie at the top.
"The goal was to not fall back and there's a strong field behind you, so it was important that I didn't slip back," said Lee, who was pipped to the Omega European Masters crown in a play-off by Thomas Bjorn last season. "I had a pretty good chance early on to distance myself from the rest of the field, but I didn't really capitalise on the back nine."
Molinari feels his game is in a good place as the Italian continued his return to form with a 68. The 32-year-old has been plagued by injury problems since making his Ryder Cup debut alongside brother Francesco in 2010, slipping from world's top 20 to No.220 as a result.
Having finished inside the top ten in Dubai last week, however, the former Scottish Open champion is continuing his rehabilitation in South Africa. "I'm very happy with pretty much everything; I am very happy with my position and my game right now," said Molinari.
England's David Horsey and home favourite George Coetzee share third on 10-under and the former was delighted with his work on the greens after an eight-under 63 on the West Course. The two-time European Tour winner had six birdies over his opening 14 holes, and rolled in a five-footer at the 15th and a 30-footer at the next to complete his scoring in a flawless round.
Alastair Forsyth, who opened with a 64, posted a more modest 70 yesterday but the two-time tour winner is well in the hunt in a share of fifth, just two shots off the pace. His fellow Scottish tour champions, Scott Jamieson and Marc Warren, were among a host of home hopefuls who missed the cut.