Murphy's number 15 jersey is taken by Leinster's Girvan Dempsey, who wins his 66th cap.
Announcing the team on Tuesday, coach Eddie O'Sullivan stressed full-back Murphy was not demoted for any particular failings in the recent defeats to New Zealand.
"I don't think he is on top of his game at the moment, and I think he would be the first to admit that," O'Sullivan said.
"I said at the start of the tour I would try and pick the best team each week."
Murphy remains on the bench to cover the back three, while Wasps fly-half Jeremy Staunton earns a place among the reserves, with veteran wing Denis Hickie omitted from the squad.
O'Sullivan was impressed with Australia in their two Tests against England, which saw John Connolly's men reclaim the Cook Cup.
"I don't know what the average score was in the first two Tests, but they look like they have hit the ground running," he said.
"Their back line are firing, they're playing some very accurate rugby and running some great lines.
"An aspect of rugby I've always admired is Wallaby back play, and I've tried to follow that myself to a fair degree.
"I think they have taken a fair bit of pressure off the Wallaby pack, and given them a chance to get their game together."
Ireland team to play Australia in Perth on Saturday: G Dempsey (Leinster); S Horgan (Leinster), B O'Driscoll (Leinster, capt), G D'Arcy (Leinster), A Trimble (Ulster); R O'Gara (Munster), P Stringer (Munster); M Horan (Munster), J Flannery (Munster), J Hayes (Munster), D O'Callaghan (Munster), P O'Connell (Munster), N Best (Ulster), D Wallace (Munster), D Leamy (Munster).
Replacements: R Best (Ulster), B Young (Ulster), M O'Driscoll (Munster), K Gleeson (Leinster), I Boss (Ulster), J Staunton (Wasps), G Murphy (Leicester).