Aiken was one of only two players in the top ten overnight to have started the tournament on the difficult East Course, having opened with a seven under 64 to be two off the pace.
And the 27 year old - seven times a winner on the Sunshine Tour - picked up regular birdies on the West Course to reach 13 under par with six holes to play.
That was one ahead of compatriot and overnight joint-leader Martin Maritz and England's Jamie Elson.
Maritz had also started one the East Course, and his blistering 62 defied the fact only four of day one's top 26 scores came on the East lay-out.
He was three under at the turn thanks largely to an eagle at the par five ninth.
Elson, who narrowly failed to keep his European Tour card last season, reached six under through 12 holes with an incredible run of five straight birdies from the fifth.
Two more South Africans - Garth Mulroy and Tyrone Mordt - share fourth on 11 under, with defending champion Charl Schwartzel amongst those a shot further back.