Hooper, who claimed the award in 2013 as well, ended Israel Folau’s run of wins, joining the full-back, George Smith and Nathan Sharpe as dual winners.
The number seven beat out David Pocock by 107 votes to win the award, with his back row partner finishing second despite missing five Tests in 2016, with his World Cup domination propelling him up the leaderboard.
Will Genia, Bernard Foley and Folau rounded out the top five in the medal count, which is voted on a 3-2-1 basis by the Wallabies players each Test, running from last year’s Chicago Test until the third Bledisloe on October 22.
The voting period included Hooper’s 50th Test, a milestone he reached in the shortest amount of time of any Test player.
Hooper, 24, was also voted the fan favourite for a remarkable fourth year in a row, with his award double answering some early season critics.
Australian Rugby Union CEO Bill Pulver said Hooper’s ascension to the top of the game was incredible for someone so young.
“Over the past twelve months, Michael has been consistently one of the most impressive players in the world, and this was never more evident than during last year’s World Cup when he combined masterfully with David Pocock to steer Australia to the final,” he said.
“Michael is still 24 but has shown than age is no barrier after having been named Australia’s youngest Test captain in 2014.
“As vice-captain of the Wallabies this year he has helped to lead the team admirably. We are excited to see what Michael and his team mates can do on the field during the coming Grand Slam tour, and we know they will be doing all they can to make us proud.”
Outside back Dane Haylett-Petty was rewarded for his consistent debut Test season with the Wallabies Rookie of the Year award, in a year with plenty of competition after 11 new players were blooded into the team.
Another back row star, Sean McMahon, beat out Hooper to take the Super Rugby Player of the Year gong, with his Rebels teammate and breakout star Reece Hodge topping the rookie poll.
Charlotte Caslick topped a sensational year, including an attention-grabbing Olympic campaign, named the Shawn Mackay Women’s Sevens Player of the Year.
Ed Jenkins was named the men’s best player, after leading the side to Olympic qualification and becoming Australia’s most-capped Sevens player.
Wallaroos captain Ash Hewson was crowned the Women’s XVs Player of the Year, after steering her team in a historic two-Test series against New Zealand, off the back of leading Sydney Uni to its second straight national championship.
Sydney Rays centre Irae Simone won the NRC Player of the Year, after a scintillating run through the domestic competition.
Australia U20 prop Tyrel Lomax, signed with the Rebels for 2017, was named the under-age side’s Player of the Year after his standout performance in the World Championships.
John Eales Medal Awards:
John Eales Medal: Michael Hooper
Wallabies Rookie of the Year: Dane Haylett-Petty
Wallabies Try of the Year: Drew Mitchell (most responsible for Adam Ashley-Cooper's try), Australia v Argentina, Twickenham Stadium, 2015 Rugby World Cup semi-final
Australia’s Choice - Wallaby of the Year: Michael Hooper
Wallabies Hall of Fame: John ‘Jack’ Ford, John Solomon, Peter Johnson
Super Rugby Player of the Year: Sean McMahon (Melbourne Rebels)
Super Rugby Team of the Year: Brumbies
Super Rugby Coach of the Year: Stephen Larkham (Brumbies)
Super Rugby Rookie of the Year: Reece Hodge (Melbourne Rebels)
Super Rugby Try of the Year: Nick Frisby (most responsible for Jake McIntyre's try), Reds v Blues, Suncorp Stadium, Round 4
Super Rugby Referee of the Series: Angus Gardner
National Rugby Championship Player of the Year: Irae Simone, Sydney Rays
Australian U20 Player of the Year: Tyrell Lomax
Shawn Mackay Award Men’s Sevens Player of the Year: Ed Jenkins
Shawn Mackay Award Women’s Sevens Player of the Year: Charlotte Caslick
Women’s XVs Player of the Year: Ashleigh Hewson
Joe French Award: Alec Evans
Nick Farr-Jones Spirit of Rugby Award: Megan and Anthony Elliot
Roger Vanderfield Award - Referee of the Year: Angus Gardner
Volunteer of the Year: Deon Norval, Uni Norths Owls Rugby Club, ACT
Lifetime Volunteer of the Year: Dougal Whitton, Canberra Royals Rugby Club, ACT
Young Volunteer of the Year (U25): Hayden Croghan, Palmyra Rugby Club, WA
Geoff ‘Bunter’ Shaw Community Coach of the Year: Kylie Dawson, Farrer Memorial Agricultural High School Rugby, Tamworth, NSW and NSW Central Norths Rugby