He joins fellow loose forward David Pocock and fullback Israel Folau as Wallabies to earn in excess of $1m per season.
Pocock is believed to be earning NZ$4.46m on a three-year deal, while Folau signed a flexible three-year contract in 2015 worth almost NZ$2.23m a year.
Hooper's contract will see him earn a high annual pay check than the top All Blacks. The 2016 collective agreement signed by New Zealand Rugby and the Players' Association noted Kieran Read would be the highest paid All Black through to the 2019 World Cup, earning about $1m per year.
Other top All Blacks were thought to earn around the $800,000 mark.
The Wallabies captain's five-year contract rivals some of the biggest given out overseas. Welsh fullback Leigh Halfpenny and ex-All Blacks No.12 Ma'a Nonu both signed deals with French club Toulon worth about $885,000 per season, former Chiefs No 10 linked up with Montpellier on a contract with over $1m per season, and Charles Piutau moved from Ulster to English club Wasps on a deal worth about $1.8m per season.