After opening the three-Test series with a rousing victory in Perth and then a loss in Brisbane in game two, the Wallabies fancied their chances of taking down the old foe.
Instead they fell to a 21-17 loss in the deciding match at the SCG, allowing Eddie Jones's men to repeat their 2016 Test series triumph in Australia.
The Wallabies were brave in attack but saw many opportunities go begging due to errors or because of England's steely defence.
They will now be licking their wounds until the opening Test of the Rugby Championship on August 7.
With a change in the tournament schedule they travel to Argentina for two Tests against the Pumas, headed by Michael Cheika who coached the Wallabies until he was replaced by Dave Rennie.
While Cheika is set to fire up the Pumas, the home side will also enter the two-match Rugby Championship swing with their tails up after besting Wales in a three-Test series.
"We were hurting last week now we're going to be hurting even more," said Hooper.
"So it's going to be a long three weeks until we play again."
A downcast Rennie refused to use his long injury list as an excuse for their Test series defeat, saying they had the team and game plan to beat England.
"We had a good enough side on the field to win," Rennie said.
"What it highlights is we're creating really good depth and you've got a guy like Nick Frost who did really well. Injuries are part of the game, you've got to find a way, haven't you?
"We just needed to turn that field position into points. I think we did enough but you've got to be clinical and take opportunities."
The Wallabies will name their Rugby Championship squad this week and will sadly be missing Samu Kerevi, who has been a stand-out over the England series.
The blockbusting centre will instead line up for Australia in Sevens at the Commonwealth Games.
Quade Cooper will make a timely return from a calf injury with the playmaker last year leading the Wallabies to five straight wins.
As well as Cooper, locks Darcy Swain, Jed Holloway and Ned Hanigan are likely to be available as well as veteran prop Scott Sio.
Rennie said NSW prop Angus Bell would be assessed after injuring his toe in his brief stint of the bench at the SCG while Test series casualties Tom Banks (arm), Andrew Kellaway (hamstring), Izaia Perese (knee) and Cadeyrn Nevill are set to miss.
While the performance left Wallabies fans frustrated just over 12 months out from the World Cup in France, Jones felt the signs were good for the Australians.
"You can see how they're trying to play," said Jones, who coached the Wallabies between 2001 and 2005.
"They've got plenty of talent, but like anything, it takes time.
"They've had a lot of injuries, they'll find their way."
