The 22-year-old Ulsterman is tied at the top of the leaderboard with Spain's Alvaro Quiros after both shot second rounds of one under par 69.
McIlroy had climbed to nine under par, but poor drives led him to bogey the 16th and 18th holes.
He said he feels a hectic year - during which he as won the US Open and risen to world number two - may have contributed to the sloppy finish.
"It was obviously not the way I wanted to finish," McIlroy said.
It could have been a bit of mental and physical fatigue. I don't feel like I'm completely 100%.
Rory McIlroy
"I got myself in a good position, hit it in the middle of the 13th fairway and had a good chance there to get to 10 under par and to finish at seven is a bit disappointing.
"I hit a few loose shots coming in that I'll have to try and eliminate tomorrow if I want to lead this tournament going into Sunday, but I'm still tied for the lead, I'm in the same position I was last night.
"I feel like I definitely could have shot a few better today but if that's my worst round of the week, it's not too bad."
The Holywood golfer said the past 10 weeks have been a "learning experience" which he is now coming towards the end of.
He continued: "It's been a learning experience for me these last 10 weeks, I know my capabilities and my limitations and I feel like I'm coming to the end of that.
"I've just got to try and get through this weekend the best I can and really give it everything and try and win the tournament to give myself a chance (of overtaking Luke Donald in the money list) going into next week.
"I just need to make sure that I have decent energy levels for the next two rounds. I might have made the season a little bit too long for myself and that's something I've got to learn from in the future.
"It's the end of the season, I'm sure it's not just me feeling like this, I'm sure a lot of guys are. It's been a long season and there's a couple of weeks left and we get to enjoy Christmas."
Meanwhile his Northern Ireland compatriot Greame McDowell is set to take a one-shot lead into Saturday's third round of the Nedbank Golf Challenge.
The Former US Open champion overcame a double-bogey seven on the 14th to card a five-under-par 67 at the Gary Player Country Club in Sun City.
I'm very happy to finish with a couple of birdies after a bit of a whoopsie on the par five.
Greame McDowell
At seven under par the Portrush man tops a crowded leaderboard, with defending champion Lee Westwood, Martin Kaymer, Robert Karlsson and Jason Dufner joint second place.
McDowell double-bogeyed par-five 14th after pulling his drive into the undergrowth, but he also had seven birdies, including two in his last three holes.
"That's exactly what I wanted," McDowell said.
"It's a pretty bunched leaderboard, which says a lot about how tough the course is when you start leaving the beaten track."
McDowell, who spent a long time on the range after the opening round, added: "I spoke to my coach Pete Cowen who told me to tighten up my backswing a bit and I felt like I controlled my ball a bit better today, so thanks Pete!"
World number one Luke Donald is five shots off the pace - a 72 left him two under tied with home favourite Charl Schwartzel.
Masters champion Schwartzel started the day tied for the lead with Westwood, but struggled to a 74 after notching up a double-bogey six on the eighth.
German Martin Kaymer said he was pleased with his 68, which featured one bogey, three birdies and an eagle on the par-five 10th.
He said: "I played well again, the same as yesterday.
"I look forward to the weekend, I think I've put myself in a good position. I had a few good weeks in China last month which gave me a bit of confidence."