On a day where England threw bodies into every tackle and tensions boiled over from the second minute, the Kangaroos ultimately kept their cool to win out.
Cameron Munster proved the difference with a game-breaking try early in the second half, after a try-less first stanza where England had the better chances.
Hudson Young also scored a second-half try, before Australia had to hold on with Reece Walsh in the sin bin for a collecting Dom Young high.
The Brisbane star could also face sanction from the judiciary, after his shoulder hit Young in the head with Newcastle's English winger in the air after spilling a bomb.
But even if he misses the third Test at Leeds next week, Australia are guaranteed to fly home with the Ashes still in their keeping.
Playing on a shorter 94-metre field at Everton's new Premier League home Hill Dickinson Stadium and with virtually no markings, England were able to get off the line fast and pressure Australia.
Tempers flared when Tino Fa'asuamaleaui and Dom Young were both sin-binned following a second-minute scuffle, as the hosts went after the Kangaroos pack.
And while it was 4-4 at halftime courtesy of penalty goals, it was England who should have walked away with more.
Young was denied once by Reece Walsh and Gehamat Shibasaki short of the line, albeit while also being collected high for the first time by the Kangaroos fullback.
He was also shielded off another grubber by Walsh, while Morgan Knowles bombed a chance to score when he couldn't capitalise on a Walsh fumble under the posts.
The Kangaroos were also scrappy, but the difference came in the fact they took their chances early in the second half.
Munster first broke them open in the 48th minute, when the Melbourne star dummied and spun his way through England's right-edge defence to score.
Moments later Kotoni Staggs leapt high to bat back a Nathan Cleary bomb, and when Hudson Young collected it and scored Australia led by 10.
Ultimately, that five-minute period proved enough, with England physical enough but unable to produce a single linebreak in the match.
"England came out and bashed us," Munster said on the BBC.
"We gave it to them on a silver plate in the first half, but the scramble in defence was really good tonight.
"When you don't complete and you defend a fair bit, there is a lot of fatigue."
After Walsh's heroics in the Kangaroos' 26-6 win in the first Test last week, it means Australia's stranglehold of the Ashes will last at least 55 years with the next potential series in 2028.
"It's really disappointing," England coach Shaun Wane said.
"I thought we had a hold of the game at times, but it wasn't enough against a really good team.
"We didn't have that killer instinct at their end, but we created a lot.
"We did a lot go good things. We asked a lot of questions of them. We started the second half poorly and they punished us. A lesson learnt, but it is a tough lesson."
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