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.
"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."