Moore gives up the starting hooker's spot to Tatafu Polota-Nau and the skippers' armband to flanker Michael Hooper but remains Australia captain.
"Tatafu has been challenging Stephen for the number two jersey for many years and his form has warranted his selection," coach Michael Cheika.
"Stephen is our captain and he'll be up to the challenge of what both Tatafu and Tolu (Latu) will bring this series."We're growing a young leadership team within our side and Michael is a key man in this. His leadership at the Waratahs has been exceptional this year..."
Hunt, who won 10 caps in rugby league before a four-year stint in the Australian Rules code, comes in for injured Queensland Reds team mate Samu Kerevi as a second playmaker at inside centre, rather than in his usual spot at fullback.
Blindside Hanigan, 22, makes up a new-look back row with Hooper and number eight Scott Higginbotham, who is recalled to play his first test since before the 2015 World Cup.
There is also a fresh look to the front row with Tom Robertson getting his first start at loosehead prop in place of the injured Scott Sio and Allan Alaalatoa his second at tighthead.
Cheika has yet to confirm his bench for the clash.
Winger Henry Speight and outside centre Tevita Kuridrani will both line up against their erstwhile compatriots and there is a possibility of another couple of Fiji-born players being named among the replacements.
A string of test regulars, including flanker Scott Fardy, centre Rob Horne and locks Rob Simmons, Dean Mumm and Kane Douglas were left out of the original squad with Cheika opting to give youth a chance in the June tests.
David Pocock is on a year's sabbatical, while his fellow openside flanker Sean McMahon has been sidelined for six weeks by a knee injury.
Australia also host Italy and Scotland during the June international window.
Team: 15-Israel Folau, 14-Dane Haylett-Petty, 13-Tevita Kuridrani, 12-Karmichael Hunt, 11-Henry Speight, 10-Bernard Foley, 9-Will Genia, 8-Scott Higginbotham, 7-Michael Hooper (captain), 6-Ned Hanigan, 5-Adam Coleman, 4-Sam Carter, 3-Allan Alaalatoa, 2-Tatafu Polota-Nau, 1-Tom Robertson
Replacements: To be confirmed
(Reporting by Nick Mulvenney, editing by Amlan Chakraborty)
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