But scores from captain James Chisholm and replacement wing Will Haywood secured the win, with Tom Morton's boot adding nine points and Aaron Morris' four.
England started brightly and went ahead with ten minutes played through Sale Sharks fly-half Morton, and he was on hand again to add two more penalties to extend the hosts' lead to 9-0 shortly afterwards.
Australia struggled to get a foothold in the game and their troubles were exacerbated when playmaker and number ten Andrew Deegan was sent to the sin-bin for talking back to Welsh referee Ben Whitehouse.
But the tourists rallied and after England centre Nick Tompkins was shown a yellow card - also for talking back to the official - Deegan returned to the pitch to get his side on the board and make it 9-3.
After a slow start to the second period, England finally made the breakthrough with just over ten minutes left to play. A break from Tompkins freed up space for Howard Packman, who in turn found Chisholm, the skipper powering over from 15 metres out.
In the last phase of play England sent passes through the hands in Harlem Globetrotter-like style, the ball eventually falling to Haywood - a late inclusion to the squad - who made no mistake from close range.
England Under 18s vs Australia
15 Aaron Morris (Bedford Blues)
14 Josh Skelcey (Northampton Saints)
13 Nick Tompkins (Saracens)
12 Max Clark (Bath Rugby)
11 Howard Packman (Northampton Saints)
10 Tom Morton (Sale Sharks)
9 Stuart Townsend (Exeter Chiefs)
1 Lewis Boyce (Leeds Carnegie)
2 Jack Walker (Leeds Carnegie)
3 Paul Hill (Leeds Carnegie)
4 Kieran Treadwell (Harlequins)
5 Charlie Ewels (Bath Rugby)
6 Joe Batley (Gloucester Rugby)
7 Will Owen (Leicester Tigers)
8 James Chisholm (Harlequins) (C)
Replacements (all used)
16 Ollie Adams (London Irish)
17 Luke Chapman (Exeter Chiefs)
18 Ciaran Parker (Sale Sharks)
19 Will Witty (Newcastle Falcons)
20 Andrew Boyce (Worcester Warriors)
21 Rory Jennings (Bath Rugby)
22 Theo Brophy-Clews (London Irish)
23 Will Haywood (Gloucester Rugby)