Lee Westwood and Scotland's Russell Knox are one shot further back
McIlroy, whose opening round of 63 had given him the early lead, began his morning round on day two with early bogeys but came back from his 7th hole of the day with a run of birdies, eventually finishing with a round of 66 to be at 11 under and enjoying a comfortable lead at that stage.
De Jonge played late in the day and joined McIlory in the lead with a birdie at his 17th hole before he bogeyed the last to give McIlory back his outright lead.
Twelve months ago McIlroy withdrew from this event at a time when undergoing a number of changes in his life and game.
He was unable to win in 2013 until a last hole victory over Adam Scott at the Australian Open appeared to give him back his mojo and the improvement has carried over to 2014.
If he were to go on and win this week McIlroy would move up four places in the world ranking to number four.
The leading Australian at the halfway stage is John Senden who added a round of 63 to be in a share of 9th position at 5 under after being in jeopardy of missing the cut after his opening round of 72.
Adam Scott is the next best at 3 under and eight shots from the lead.