McIlroy had an eagle and got to 15-under 169 after 10 holes for a two-shot lead over Louis Oosthuizen, who was in his group, and Richard Green of Australia, who played 11 holes.
Thomas Levet of France, one of 17 players to complete the third round, was the clubhouse leader with a 10-under 206 following a 66.
The European Tour event has been affected by morning fog, which has resulted in the loss of six hours of play.
The second round, which began Friday, was not completed until Saturday morning.
When play was suspended for the day Saturday, only six of the 23 groups had completed their rounds. The remaining 51 players will return to the course to finish the third round on Sunday morning.
The 19-year-old McIlroy had finished his second round at 4-under 68.
It would be huge if I win here ' one of the best events on the tour. If I could pull it off, it would be absolutely fantastic. But right now, I have got the tee shot on the 11th tomorrow morning on my mind, and thats all I can do, McIlroy said.
Three-time champion Ernie Els missed the cut by a stroke after rounds of 71 and 73 left him at even-par 144.