Hooper would lead the rebuilding team into back-to-back tests against the All Blacks when the southern hemisphere's Rugby Championship kicks off later this month and then onto the 2019 World Cup in Japan, his coach Michael Cheika said.
The abrasive back rower has long been groomed to step up to the role, having led the side throughout the 2014 season when Moore was injured and twice during the recent June internationals when the hooker was benched.
In 2014, as a raw 22-year-old, he became the youngest Wallabies captain after Ken Catchpole and guided the team to a whitewash victory over France in his first series in charge.
Now 25, Hooper has 68 tests to his credit and played a key role in Australia's run to the 2015 World Cup final against New Zealand when he and fellow openside flanker David Pocock teamed up in a powerful back row combination.
"It's a huge honour to step into this role," Hooper told reporters at Sydney's Olympic Park on Wednesday.
"I've learnt a lot from Stephen... Having him for the next four months is so critical for the team and so helpful for me.
"I'm so excited about learning and getting better in this role, there's a lot of good times ahead."
Hooper will lead the Wallabies during a tough period for Australian rugby and faces a baptism of fire against an world champion All Blacks side smarting from being held to a draw in their recent series against the British and Irish Lions.
The teams meet in Sydney on Aug. 19, with the second match of their Bledisloe Cup series in Dunedin a week later.
POCOCK TO RETURN
Australia's provincial teams were unable to win a single match against New Zealand opponents during the Super Rugby season, while the Wallabies drew scathing criticism for their performances during the June internationals.
After overcoming Fiji, they lost at home to Scotland and suffered a huge scare against lowly Italy.
Hooper's fitness to captain the Wallabies will also be questioned in some quarters, with former skipper and world class flanker Pocock set to return to the national setup next year after taking a year-long sabbatical.
Pocock could put pressure on Hooper's hold over the starting number seven jersey and is seen by some pundits as the ideal man to lead the Wallabies to Japan.
Cheika, however, saw no conflict in managing the two opensides.
"It's not like those two guys haven't been in the same squad before," he told reporters.
"Right now David's having time off. He'll have to come back in, earn his stripes, get himself back in the side. I don't see any type of issue with the combination of players, whatsoever."
Hooper's leadership has also been queried after a difficult season at provincial level, with the New South Wales Waratahs slumping to their worst Super Rugby season in a decade under his captaincy.
Former Waratahs coach Cheika, who appointed Hooper captain of the Sydney side during their run to the 2014 title, has remained a staunch supporter, however.
"When you're asked to be in a leadership position, the biggest prerequisite is respect," Cheika said. "All players in Australian rugby... they respect Michael Hooper."
(Writing by Ian Ransom; Editing by John O'Brien)
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