Scott shot 2-under-par 70 for a two-round total of 12-under 132. McIlroy, playing in the morning and avoiding the rain and storms that later hit the course, had a 65.
Scott and McIlroy will play together on Saturday in the third round.
"It was always going to be a day where you just had to hang on," Scott said of the tough conditions. "He (McIlroy) is one of the best players in the world so I'm going to have to bring my best game."
Australian Richard Green shot 66 and was three strokes behind Scott, who is trying to add the Australian Open to his Australian PGA and Australian Masters titles to become the second player after Robert Allenby in 2005 to capture the Triple Crown of Australian majors.
McIlroy felt lucky to have escaped the worsening conditions.
"The weather wasn't as bad as we thought it was going to be and the wind didn't pick up," he said. "So I knew we could take advantage of that, and the greens were a little bit softer as well."
Defending champion Peter Senior had an 81 Friday and did not make the cut.
Kevin Streelman, who played with Matt Kuchar in the American team at last week's World Cup, retired on the fourth hole due to an eye infection. Playing for the first time in Australia, he was later taken to hospital for treatment.
Streelman, playing with Scott and Jason Day, shot 70 in the opening round Thursday and began Friday's round with a birdie.
But as his eye condition worsened, he had a 5 on the par-3 third and a bogey on the par-4 fourth before deciding to retire.
"It's pretty rough right now but we'll see what we can do," Streelman said. "The doctor said it was pretty badly infected.
"I've been trying to do some drops but I started getting dizzy and it's the first time I've ever (withdrawn) at a tournament ... I'm really sad to do it."
Streelman won the PGA Tour's Tampa Bay Championship in March and finished second with Kuchar behind Day and Scott in the team event at the World Cup at Royal Melbourne.