That denied Steve Hansen's side a world record 18th straight win, but the All Blacks - hosts for the 2017 Lions tour - responded to the setback in impressive fashion.
They welcomed Australia to Eden Park and racked up six tries in a 51-20 victory to retain both the Bledisloe Cup and the bragging rights.
And Hooper - the Wallabies' youngest skipper since 1961 - admitted the hefty defeat was difficult to stomach, as they head into a two-week break from Rugby Championship action.
"It was tough," he told Australian Fox Sports. "To go through Auckland airport and see all the Kiwi jerseys and all the Kiwi supporters really happy and our supporters unhappy, it was tough to come back as a group.
"But we can rebuild, we get away for a week and mentally, really recover.
"I think the coaches get a chance to have a look at the first two games and look at how people have been performing and we'll get a chance to get away from it which will be nice and mentally relax.
"There'll be a fair bit of down-time over the next week but I'm sure the coaches will be ringing the tape and trying to get the best out of what we have at the moment."