The fourth Rolex Series event of the year was shortened to 54 holes after Friday's play was cancelled following the death of Her Majesty Queen Elizabeth II on Thursday.
Wentworth held a two-minute silence on Saturday morning and players wore black ribbons.
McIlroy's round got going with an eagle at the fourth and he added birdies at the eighth, 11th, 12th, 17th and 18th. The birdie at the 17th came after his tee shot looked gone, only for the ball to come back out of the trees after an agonising few seconds.
But for McIlroy, some of the pars were just as memorable.
He said: "Par putt on 16 was huge. Par putt on 13 was big as well. Even that little one at the last, I put myself in a good spot and sort of had it slide by five feet. To hole that one and just get one closer to the leader going into tomorrow was really important.
"I thought my putting today was really good, and that's really what's kept me in the tournament."
McIlroy is chasing a double as he leads the DP World Tour Rankings in Partnership with Rolex having won the FedEx Cup last month.
He added: "I had that great finish in the States, I wanted to turn my attention to here and win the Rankings. It would be great to win it for the fourth time, and I didn't want to let up.
"I've got a great chance tomorrow to win this prestigious event but also to extend the lead in the Rankings, and then we'll go to Italy and try and do it all over again.
"I gave myself a couple of days off from East Lake but my attention quickly turned to, not just this event but the rest of the season, and I'm keeping myself quite busy over the next couple of months.
"I want to finish the year off on a high. I finished the season in the States off on a real high, and I want to do the same over here.
"I want to try to get that double. So a good day tomorrow would put me well on my way to doing that."