Chasing the game in the second half, England introduced the dangerous Gloucester duo of Freddie Burns and Jonny May and chances duly followed as Mark Mapletoft's side embarked upon a spirited fightback.
However, the gap proved to be too large to breach, begging the question what would have happened if the Gloucester duo had started the game alongside their club team mate Shaun Knight?
Australia were liveliest in the opening 10 minutes, making the half-breaks that established an early platform before To'ouma opened the scoring with a penalty.
But No.2 seeds England fought their way into the game as well as controlling set pieces and some surging forward play put them on top before the ball went wide for Smith to grab the opening try of the game and his first score of the tournament.
His opposite number Toua, meanwhile, has also been a threat all through the JWC and edged Australia back in front with To'ouma converting.
But despite Homer's first successful penalty pegging them back to 10-8, Australia exploited their attacking positions in the 10 minutes before the break to open up a 12 point lead.
Morahan's cut back to the line and To'ouma's assist gave them a second try and the Junior Wallabies came close to a third before settling for To'ouma's second penalty.
England battled back after the interval, defended stoutly and their replacements all added value, Lee Imiolek making an impact in the tight and Freddie Burns lively at fly half.
A potentially try-scoring chip and chase from Burns was flapped away over the dead ball line - potentially a penalty try award - before Homer drilled over three more points to reduce the deficit.
But England just fell off too many tackles and conceded territory - To'ouma adding his third penalty - before coming again late in the game with Smith, Homer and Burns all lively.
They allowed Sitauti to get away for a score three minutes from time, though, before May responded by shrugging off tackles in the final move of the match to make the line for the final score.
Tom Homer (London Irish); Christian Wade (London Wasps), Andrew Forsyth (Leicester Tigers), Tom Casson (Harlequins), Sam Smith (Harlequins); Rory Clegg (Harlequins), Charlie Davies (Stade Francais); Joe Marler (Harlequins), Jamie George (Saracens), Shaun Knight (Gloucester), Calum Green (Leicester Tigers), Charlie Matthews (Harlequins), Jamie Gibson (London Irish), Jacob Rowan (Leeds Carnegie, captain), Jackson Wray (Saracens).
Arthur Ellis (London Wasps) for George 53, Lee Imiolek (Sale Sharks) for Marler 53, George Kruis (Saracens) for Welch 55-65, Will Welch (Newcastle Falcons) for Wray 50, Sam Harrison (Leicester Tigers) for Davies 41, Freddie Burns (Gloucester) for Clegg 54, Jonny May (Gloucester) for Forsyth 41.
Scorers: Tries: Smith, May. Penalties: Homer 2.
Luke Morahan; Dominic Shipperley, Kimami Sitauti, Robbie Coleman, Aidan Toua; Matt To'omua, Nic White; Salesi Manu, Siliva Siliva, Paul Alo-Emile, Phoenix Battye, Greg Peterson, Ed Quirk, Liam Gill, Jake Schatz (captain).
Sam Roberson, Cruz Ah-Nau, Luke Jones, Lochy McCaffery, Ian Prior, Jono Lance, Greg Jeloudev.
Scorers: Tries: Toua, Morahan, Sitauti. Conversions: To'ouma 2. Penalties: To'ouma 3.
Content courtesy of RFU