The crash on the fifth lap put paid to a solid showing at home, having qualified third behind Fabio Quartararo and Marco Bezzecchi.
Although the Yamahas had one-lap pace, their race pace couldn’t match Aprilia nor Ducati.
Miller finished fourth in Saturday’s sprint before a slow start to Sunday’s grand prix saw him drop back to sixth before crashing.
“Deflated. That’s the way it goes, that’s motorcycle racing, that’s how it happens sometimes,” said Miller, post-race.
“It was all around a good weekend. Solid pace in every session, solid pace in the race.
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“The balance, I just was struggling a little bit with the balance of the bike throughout the race – my part of the race anyway. Especially going into [turn] six, it was vibrating and transferring to the front I was having to force it quite a bit to go in.
“I kind of felt it three laps before I binned it. When it finally went, I kind of had some warning signs there, but I was in the group and tried to push through it.
“I was trying to wait until the group kind of came back, trying to nurse the tyre, and save it in the areas I could – exit of the last corner, exit of [turn] 3. Unfortunate.”
Miller offered an apology to his fans, who turned up in their droves for Sunday’s race despite the threat of inclement weather.
“Obviously devastated for the Aussie fans because it turned into a nice day,” he said.
“We’ll go forwards. Positive weekend, good speed all around. It was a good weekend in Indonesia. I haven’t been able to put the points on the board during the grand prix race.
“We’ll go back. We’ve got to be better next weekend at Malaysia and try finish this year out strong.”
MotoGP continues at Sepang for the Grand Prix of Malaysia on October 26-28.
Miller crashes as MotoGP crowns first-time Phillip Island winner
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