Jones, who took Australia to the final of the 2003 World Cup on home soil, is now 0-3 in his second stint in charge following the 38-7 loss at the Melbourne Cricket Ground.
The All Blacks sealed the Rugby Championship title and also retained the Bledisloe Cup, the annual trophy contested by the trans-Tasman nations, for a 21st year in succession, adding to Australia's gloom.
After a thrashing by South Africa and a tight loss to Argentina, Australia's third loss was arguably their most galling under Jones, coming in front of a massive home crowd of 84,000 at the Melbourne Cricket Ground.
"You know, they've worked really hard, but we know it's not good enough," Jones said of his players.
"We apologise to all the fans and it's not good enough, but that's my fault. That's my responsibility and I'll take it on the chin.
"Look, it's a terrible result. I take full responsibility for it. But I'm pleased the way the players applied themselves and first 20 minutes and the first bit of the second half."
Australia were kept scoreless for over 70 minutes following Rob Valetini's converted try and were made to pay dearly by the All Blacks for giving up a yellow card in each half.
The night was further soured with a serious Achilles injury to Allan Alaalatoa, while fellow prop Taniela Tupou suffered an apparent rib injury.
In a further blow, Jones revealed that co-captain and veteran flanker Michael Hooper's calf injury was severe enough to put him in doubt for the World Cup.
Despite the Wallabies' woes, Jones said he had seen enough from them against the All Blacks to know they could be "a bloody good team".
"I've coached teams like this before and you can turn it around," he said.
"It doesn't look like it at the moment and you're sitting there thinking, 'Shit, what's this bloke talking about?'
"So for the fans, they got to keep being hopeful. Keep praying, whatever God they've got, keep praying to that we will turn it around.
"Don't worry, we will."