They clashed in the first two Tests of the British & Irish Lions tour in the summer and, with David Pocock remaining at home to give his injured knee more time to recover from reconstruction surgery, will lead the breakdown trio in Europe.
These latest accolades for Hooper add to a collection that already includes the Super Rugby Player of the Year and Castrol EDGE Strongest Performer Award in 2013; Qantas Wallabies Rookie of the Year in 2012; and Under 20s Player of the Year in 2011.
Hooper received 297 votes from his peers, more than 100 votes ahead of his nearest rivals, Wycliff Palu on 185 votes and Israel Folau on 177. Adam Ashley-Cooper and Christian Leali'ifano completed the top five with 131 and 102 votes respectively.
The John Eales Medal, named after the former Wallaby captain, comes just over a year after Hooper made his Test debut against Scotland, during the match played in cyclonic conditions in Newcastle, and follows his third placing for the John Eales Medal in 2012. Hooper polled in all but one of the 14 Tests during the voting period from last year's Spring Tour to the third Bledisloe Test last weekend.
He becomes the fourth flanker to win the John Eales Medal, behind George Smith (2002 and 2008), Phil Waugh (2003) and David Pocock (2010).
Hooper's Waratahs' teammate, Israel Folau, was named Qantas Wallabies Rookie of the Year, following a debut season that saw him score two tries in his first match in the opening Test against the Lions, and a further five tries since.