In what will surely be the key fixture in Pool D at the Rugby World Cup, Wales got the better of a strong-finishing Australia 29-25, having led 23-8 at the break.
Tries from Dane Haylett-Petty and Hooper himself set up a tense finish, but the Wallabies could not quite wrestle back control of the match.
Hooper was disappointed but keen to move on quickly, knowing Australia cannot afford to spend too long reflecting on a defeat that likely sends them into the same side of the draw as England and New Zealand.
"It was a close game between two very willing teams and it came down to the wire," he said.
"It was 17-6 [in the second half] - we had the momentum, we just gave away too many in the first half. In particular the back-to-back points really hurt us.
"Congratulations to Wales for holding us out.
FULL TIME here in Tokyo.
— Wallabies (@wallabies) September 29, 2019
"We'll review it now. Recovery is key. We'll review it pretty hard, but in this format of competition, you've got to move on pretty quickly."
Coach Michael Cheika offered a blunt assessment of Australia's defeat, adding: "What went wrong? We just lost by a couple of points - it was a tight contest and that's the way it goes sometimes."
Photo Getty Images Caption: Australia captain Michael Hooper