McIlroy, who was two under at the tournament, was seven strokes behind leaders Daniel Rodriques (64) and Rasmus Neergaard-Peterson (66), who had a total of 9 under at 133.
The leading pair was one shot ahead of third-place Min Woo Lee, who shot 65 on Friday.
Adam Scott (66) was tied for fourth with Cameron Smith (65), who avoided adding to his tally of seven consecutive missed cuts. Scott and Lee played in the same trio as McIlroy.
McIlroy started the day with 1 over after a 72 on Thursday, finishing tied for 57th and seven shots behind the leaders. At the time, that was just one shot inside the expected 2-over boundary.
He birdied Friday and had eight pars on his front nine, then made four more pars before bogeying the par-5 14th. He missed the fairway to the right of the tee and ended up under a tea tree. McIlroy then whiffed on his next shot when his club got stuck in a branch, but he recovered to make a 6.
That put him outside the 36-hole cut, but he birdied the next hole, the par-3 15th, to bring himself back to even par and safe at that point.
He parred the 16th to stay level and then made perhaps his shot of the tournament – from the patchy rough on 17, this time swinging through a small bush, where he tapped in for birdie after a long eagle putt went just wide.
That moved McIlroy to 1 under in the tournament and about 20 places higher in the leaderboard, making him safe for the weekend, especially after he birdied the 18th.
“With the wind, it played like a different golf course today,” McIlroy said. “I definitely haven’t played my best the last few days, but it was nice to finish the way I did. I’m happy to be here this weekend… seven isn’t that far back.”
Of his scented shot from under the trees, McIlory said: “To be honest, I can’t remember the last time I hit a shot in the fresh air. Not one of my finer moments, but nice to be able to come back on the last few holes.”
Co-leader Neergard-Peterson missed the cut at the Australian PGA Championship last week. at Royal Queensland in Brisbane.
“I definitely feel like I’ve proven over the last year that I have the level to compete here and be right in the thick of it on Sunday,” Neergard-Petersen said.
The highlight of Australian Lee’s second round came when he holed out with a 9-iron from 176 yards for Eagle on the par-4 10th, raising both arms and waving them in an airplane-like celebration.
“I know it was just random, but it just felt good,” Lee said. “It was a big crowd, so I just did random things.”
McIlroy, whose pre-tournament press conference included comments that Royal Melbourne was not the best sand track in the city, had a wild opening round with six bogeys and five birdies.
McIlroy, the Race to Dubai winner who completed his Grand Slam career when he won the Masters this year, is making his first appearance at the Australian Open since 2015, having won it in 2013.
The winner of the Australian Open, the second event on the European tour’s new tournament schedule for the end of this year and 2026, will receive a Masters exemption next year. And the top three finishers not yet exempt will qualify for The Open in 2026 at Royal Birkdale.
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