Hooper, at 22, takes over the team captaincy after Stephen Moore was ruled out for the rest of the year with a cruciate knee ligament injury.
Not since great Trevor Allan became a 21-year-old skipper in 1947 has an Australian Test team been led by a younger player.
The Australian Rugby Union said Jimmy Flynn remains Australia’s youngest Test captain, leading his country at the age of 20 in 1914.
Wallaby coach Ewen McKenzie said openside flank Hooper had the right leadership qualities to skipper the Wallabies.
“It’s a massive honour to captain your country and I’m confident Michael has all the right leadership qualities to lead this team moving forward,” McKenzie said.
“He’ll undoubtedly bring his own unique personality to the way things are done, but we wouldn’t have recognised him in a leadership capacity at the beginning of this series if we didn’t think he had to the ability to step into this role.
“I couldn’t have been more impressed with his performance on the weekend after Stephen Moore went down [in the 50-23 win over France at the weekend], so we know the added responsibility won’t impact the high-level of play we all expect from him each week.”
Hooper’s elevation to captain continues a remarkable four seasons where he has won most significant individual awards, including the John Eales Medal in his second year of international rugby in 2013.
Hooper also won the 2013 Australian Super Rugby Player of the Year and was the Wallabies Rookie of the Year in 2012.
Since debuting against Scotland in 2012, Hooper has been chosen in the starting side for 24 of his 29 Test appearances.
With the Wallabies having won the opening Test in Brisbane, France must win this coming Saturday’s second Test in Melbourne to keep the three-match series alive.
Prop James Slipper, who turned 25 on Friday and played his 50th Test last weekend, joins Adam Ashley-Cooper as the team’s two vice-captains under Hooper.
McKenzie said Hooper will also step up to shape how this team functions off the field.
“As a group, we’ve clearly defined expectations around team culture and Michael will play a significant role in delivering that within the group,” the coach said.
“However, no one player has a mortgage on leadership and we’ll be expecting a number of guys within the group to lead.
“I was really pleased with the contributions Adam [Ashley-Cooper] made to this group as vice-captain and I’m confident James Slipper will also step-up to have a similar impact.
“James has already demonstrated the capacity to lead by guiding the Reds to four victories from his five Super Rugby games as captain in 2013.
“He’s also been one of Australia’s most consistent performers across 50 Tests and is extremely well-respected within the group.”