New prop Peter Borlase, who arrived from Canterbury last Thursday, will join Varley and Wian du Preez in the province's starting front row.
The game will also see the return of centre Sam Tuitupou after a three-week suspension since last month's Heineken Cup defeat to London Irish.
The replacements bench features Academy players Conor Murray (21), Mike Sherry (22) and Brian Hayes (20).
Australia have arrived in Limerick on the back of a 35-18 defeat to England at Twickenham. Assistant coach Jim Williams, a former Munster captain and assistant coach, has fond memories of his seven years with the province.
Looking forward to the match, Williams said: "It'll be great. It's an important step for us coming off a disappointing loss against England. These boys started off well the other week against Leicester so they'll want to keep that going.
"There'll be plenty of passion on both sides, our boys are gelling well together and they're going to come up against a bunch of guys that want to play for each other so it will be a great tussle."
The selected Australian team is chasing their second midweek win in a fortnight after beating Leicester Tigers 26-15 at Welford Road last Tuesday.
Saia Faingaa replaces the injured Huia Edmonds (shoulder) in the tourists' front row and there are two other changes to the starting pack, with prop Ben Daley and lock Dean Mumm getting call-ups.
In a reshuffled back-line, Lachie Turner has moved to full-back and Sevens star Luke Morahan will make his first start for the Wallabies on the left wing. The Waratahs' Berrick Barnes and Luke Burgess continue as the starting half-backs.
Australia head coach Robbie Deans added: "This is another great opportunity for these guys to get as close to Test rugby as you'll get.
"We're playing against teams full of international players and this week will be tougher again.
"Munster have a history of taking international scalps. Their combinations are more like international ones than provincial, and this is will be a great challenge for us."
Tuesday's encounter will be the fifth meeting between the two sides, with Munster securing three previous wins over the Australians in 1967, 1981 and 1992.
* Tickets for the game are available here and can be collected on the night. Alternatively tickets will be available to purchase from the Ticketmaster outlet at the Hassett's Cross corner of Thomond Park from 5pm.
MUNSTER: Johne Murphy; Doug Howlett, Keith Earls, Sam Tuitupou, Denis Hurley; Paul Warwick, Duncan Williams; Wian du Preez, Damien Varley, Peter Borlase, Billy Holland, Ian Nagle, Peter O'Mahony, Niall Ronan, James Coughlan (capt).
Replacements: Mike Sherry, Stephen Archer, Brian Hayes, Tommy O'Donnell, Conor Murray, Scott Deasy, Barry Murphy.
AUSTRALIA: Lachie Turner (NSW Waratahs); Rod Davies (Queensland Reds), Pat McCabe (Brumbies), Anthony Faingaa (Queensland Reds), Luke Morahan (Queensland Reds); Berrick Barnes (NSW Waratahs) (capt), Luke Burgess (NSW Waratahs); Ben Daley (Queensland Reds), Saia Faingaa (Queensland Reds), Salesi Ma'afu (Brumbies), Dean Mumm (NSW Waratahs), Rob Simmons (Queensland Reds), Scott Higginbotham (Queensland Reds), Matt Hodgson (Western Force), Richard Brown (Western Force).
Replacements: Tatafu Polota-Nau (NSW Waratahs), James Slipper (Queensland Reds), Van Humphries (Queensland Reds), Pat McCutcheon (NSW Waratahs), Nick Phipps (Melbourne Rebels), Matt Giteau (Brumbies), Peter Hynes (Queensland Reds)
Referee: Bryce Lawrence (New Zealand)
Assistant Referees: Alan Lewis, David Wilkinson (both Ireland)
Television Match Official: Tony Redmond (Ireland)