Hooper polled 91 points in the player-led vote, finishing just three points ahead of last year's winner Marika Koroibete, while James Slipper was third with 79 points.
Nic White (61 points) and Reece Hodge (56) rounded out the top five.
In a pandemic-reduced season, the Wallabies played six tests, winning one, drawing three and losing two.
"On behalf of the Australian Rugby community, I would like to congratulate all of our winners throughout the Rugby Australia Awards series," Rugby Australia interim boss Rob Clarke said.