SYDNEY, November 29, 2013 (AFP) - The reigning Masters champion shot a two-under-par 70 to move to 12 under par and two strokes clear of Northern Ireland's McIlroy who posted a seven-under-par 65 and finished 10 under par.
It was the fourth time McIlroy had shot 65 this season, and just one stroke more than the 64 he recorded in August's FedEx Cup opening Deutsche Bank Championship in Boston.
After what he described as a "wasteful" first day of 69, the current World No. 6 McIlroy had nine birdies in his round and only 25 putts.
Scott headed into the second day leading by three shots and extended that to five when he birdied the first and then holed a 50-yard chip shot for a birdie at the third hole.
He then double bogeyed the fourth and dropped a shot at the next to find himself trailing a stroke behind McIlroy.
However, the Australian regrouped in the windy and sometimes rainy conditions to grab back-to-back birdies at seven and eight and also at the 12th and 13th holes, finishing bogey, birdie, bogey and just missing by millimetres a birdie at the last.
"It was a tough afternoon with plenty of good stuff in there but then I made a few mistakes in the tricky conditions but overall it was pretty good and given how difficult it was, I was pleased I held it together pretty well," he said.
"It was a like a five club wind on a few of the earlier holes so it was a day where all you could do was just hang on and try and hit as many good shots as possible.
"And while I managed a good few birdies, if you were slightly off the bogeys were easy to come by."
In a dream match-up, Scott will now play the third round in the company of McIlroy.
And while Scott has already tasted success four times this year his 24-year old rival, apart from defeating Tiger Woods earlier this month in China, is still looking for a first Tour victory in 2013.
"I'm really looking forward to playing alongside Rory and it's another good leader board, and like I said all week it's going to be a tough one to win," Scott added.
"There are plenty of guys in the mix and I am going to have to play some golf as there is plenty of birdie opportunities out there."
Australia's Richard Green is in third place after a round of 66 for a nine under par total.
Leading scores after the second round of the Emirates Australian Open at Royal Sydney Golf Club (par 72) on Friday.
132 - Adam Scott (AUS) 62 70
134 - Rory McIlroy (NIR) 69 65
135 - Richard Green (AUS) 69 66
136 - Matthew Jones (AUS) 68 68
138 - Alistair Presnell (AUS)67 71, Josh Younger(AUS) 69 69, Leigh McKechnie (AUS) 73 65, Brady Watt (AUS) 68 70
139 - Aron Price (AUS) 70 69, Max McCardle 68 71
140 - Scott Arnold (AUS) 70 70, Jamie Arnold (AUS) 72 68, Ryan Yip (CAN) 65 75
141 - Bryden Macpherson (AUS) 71 70, John Senden (AUS) 73 68, Geoff Ogilvy (AUS) 75 66, Rhein Gibson (AUS) 71 70, Nathan Holman 69 72, Aaron Baddeley (AUS) 67 74, Adam Bland (AUS) 69 72, Jason Scrivener (AUS) 67 74, Cameron Percy (AUS) 71 70, David McKenzie (AUS) 66 75, James Nitties (AUS) 70 71