McIlroy was among the entire afternoon session groups that could not finish their round in the $3 million event on Friday following a two hour, 50 minutes fog delay in the morning.
He returned to the course Saturday sitting at 10 under par after 11 holes, and then made five birdies in the remaining seven holes to finish on 15-under 129.
Welshman Jamie Donaldson, who finished his second round on Friday, was second, two behind McIlroy at 13 under par.
China’s Li Haotong was in sole third place at 12 under par, with a group of four players at 11-under, including South Africa’s world number 29 Branden Grace.
The Northern Irish world number 11, who finished with three birdies in his last three holes, said: “The conditions were very conducive for scoring. Especially with the greens being the way they were in the morning, they are just a bit better.
“So if anything, it was nice to stop yesterday and get back again this morning. The greens were pure and just gave myself chances. Glad I was able to convert a few.”
A new record was set for the cut, with 70 players tied at five under par or lower making it to the final two rounds. The previous low cut record was three under par in 2001 and 2007.
The players started their third round at 1100 local time (0700 GMT), going out in threeballs from both tees.