SYDNEY, 28 Nov 2014 (AFP) - The Australian left-hander, who won his national open in 1998 and 2011, swept to the front with two birdies in his final four holes at The Australian course to finish at five-under 66.
Dallas-based Chalmers, at five-under 137, held a one-shot lead over McIlroy, Australians Adam Crawford and Todd Sinnott and American Conrad Schindler heading into the weekend rounds.
Players sported black ribbons during Friday's second round in respect for Test cricketer Phillip Hughes, who died Thursday after being knocked unconscious by a ball in a domestic game in Sydney this week.
"I'm really pleased, seven birdies, a couple of bogeys, but it's very early to be thinking about what's going to happen on Sunday night, considering who's right behind me and playing well," Chalmers said.
World number one McIlroy had a rollercoaster round containing an eagle, six birdies, six bogeys and just one par on the homeward nine holes, but is well placed at the halfway stage to defend his title.
McIlroy overhauled Scott with a birdie at the final hole to win last year's tournament at Royal Sydney in what was his only 2013 tournament success.
"I felt like I had an opportunity today to shoot a good one and put a little bit of space between myself and the rest of the field, but it didn't really turn out that way," McIlroy said.
"A few too many mistakes and it was pretty tricky out there. Swirling quite a bit, which made it hard for club selection.
"I was happy with how I finished, I picked up shots in four of the last five holes and I'm still in a good position heading into tomorrow."
Scott bounced back with a five-under 66 in the morning groups to lie joint ninth on two-under and three shots off the lead.
The world number three recovered from a shaky three-over 74 in the opening round to grab an eagle and three birdies in an unblemished second round.
"Yesterday I got off to a bad start, in the wind it was tricky and I didn't scramble when I had to early in the round and it was slipping away from me," Scott said.
"Today it didn't start much better, I was scrambling, but I scrambled well, and then all of sudden I made eagle at 14 and momentum was on my side then.
"It's an incredible different feeling of being two under to two over and about how you feel about the state of your game," Scott said.
US Masters runner-up Jordan Spieth, the overnight leader, fought back with a birdie at the last for a one-over 72 to be three-under overall for the tournament and in joint sixth place with Australians Geoff Drakeford and Brett Rumford.
"I got away with some shots yesterday and hit more greens in regulation but today my irons were off and short irons were off," Spieth said.
"I'll save the best stuff for the weekend."
American Jamie Lovemark went one better than Scott and Chalmers to snatch the course record with a 65 at the Jack Nicklaus-designed layout at The Australian, which was revamped four years ago.
Leading scores after the second round of the Australian Open at The Australian course (par-71) in Sydney on Friday (Australia unless stated):
137 - Greg Chalmers 71-66
138 - Rory McIlroy (NIR) 69-69, Adam Crawford 69-69, Todd Sinnott 71-67, Conrad Shindler (USA) 70-68
139 - Jordan Spieth (USA) 67-72, Geoff Drakeford 69-70, Brett Rumford 70-69
140 - Robert Allenby 71-69, Rod Pampling 73-67, Jake Higginbottom 71-69, Adam Scott 74-66, Rhein Gibson 70-70, Richard Green 69-71
141 - Scott Gardiner 68-73, Matthew Griffin 72-69
142 - Jason Norris 73-69, David Bransdon 72-70, Nick Cullen 73-69, Jamie Lovemark (USA) 77-65, Lincoln Tighe 70-72, Matt Jager 72-70, Jin-ho Choi (KOR) 74-68, John Senden 73-69
143 - Stephen Dartnall 72-71, Aaron Townsend 73-70, Boo Weekley (USA) 72-71, Ashley Hall 73-70, Oliver Goss 71-72, Andrew Evans 75-68, Cameron Smith 73-70, Sung-Hoon Kang (KOR) 73-70, Josh Younger 71-72, Joon-woo Choi (KOR) 72-71, Bryden Macpherson 70-73, Aron Price 68-75, Rohan Blizard 70-73, Antonio Murdaca 70-73
Selected scores:
144 - Brendon De Jonge (ZIM) 69-75, Patrick Rodgers (USA) 70-74
145 - Garrett Sapp (USA) 73-72
146 - Kyle Stanley (USA) 74-72, Jin Jeong (KOR) 71-75
147 - Wisut Artjanawat (THA) 74-73, Daniel Woltman (USA) 73-74, Rory Hie (INA) 72-75
148 - Achi Sato (JPN) 69-79
149 - Ryan C Carter (USA) 73-76
150 - Do-hoon Kim (KOR) 77-73, Kyong-hwan Lee (KOR) 74-76, Tommy Mou (TPE) 76-74, Xinyang Li (CHN) 77-73
151 - Hyo-won Park (KOR) 77-74, Minghao Wang (CHN) 74-77, Devin Daniels (USA) 73-78, Gunn Yang (am, KOR) 73-78
152 - Jordan Krantz (CAN) 80-72, Deuk-hee Park (KOR) 77-75, Yi-keun Chang (KOR) 74-78
153 - Bi-o Kim (KOR) 76-77, Ju-hyuk Park (KOR) 74-79
154 - John Young Kim (USA) 73-81
155 - Wen-yi Huang (CHN) 78-77, Zac Blair (USA) 76-79, Chirat Jirasuwan (THA) 75-80
158 - Michael Im (KOR) 83-75
159 - Jin Zhang (CHN) 78-81
165 - Sam Yi (USA) 79-86
167 - Weiyu Zhu (CHN) 84-83
Final cut was made at +4 (146), 76 players made the cut