South African referee Marius Jonker ordered it to be re-set twice before awarding Australia a free-kick at the third scrum.
England started poorly, a series of unforced errors handing the Wallabies a 6-0 lead in as many minutes.
Tom Rees was penalised for going off his feet at a ruck, Giteau landing the penalty, while Lee Mears threw a risky long line-out for Danny Care, and Armitage put a nervous kick out on the full.
When captain Steve Borthwick was caught offside running straight through a line-out, Giteau duly doubled the visitors' lead.
If that was bad enough for the watching Johnson, the sight of Giteau motoring onto an overthrown line-out and into wide open spaces would hardly have brightened the England manager's mood.
Fortunately for the hosts, Giteau's pass was knocked on by skipper Mortlock.
Cipriani missed his first shot at goal when George Smith was penalised at the breakdown, but the 21-year-old fly-half brought the crowd to their feet with a tantalising glimpse of his talent.
Cipriani made two superb breaks but was off target with some of his kicking
Spotting two Australian forwards ahead of him, Cipriani surged between them and then left Luke Burgess on his behind before releasing Riki Flutey.
Flutey was snared but the ball was moved left to Mears, only for Giteau to force the hooker into touch in the left corner.
England's first points came instead from an unlikely source, Armitage sizing up his options before landing a speculative drop-goal from 35m.
But the hosts' indiscipline continued to undermine them, Vickery's hand in a ruck gifting Giteau another penalty before the fly-half made it 12-3 when England strayed offside trying to repel waves of Australian attacks.
The red rose pack found some momentum as the first half drew to a close, their tight forwards finally making some inroads.
Prop Andrew Sheridan was unable to ground the ball after a superb last-ditch tackle from Burgess, before Mears was again denied after an offload from Matt Stevens - temporarily on for Sheridan.
But when the ball was recycled, Borthwick drove Easter over from a metre out.
Cipriani was again off target with the conversion, but his penalty a minute before the break, and a missed attempt from Giteau, left England only a point adrift at the interval.
Cipriani's mixed afternoon continued on the resumption though, another scintillating break between two Wallaby forwards preceding a horrible missed drop-goal from barely 15m that Jonny Wilkinson would have landed in his sleep.
We need to improve basics - Johnson
He then missed another from further out, but England had already been awarded a penalty and this time the youngster was on target to put England in front for the first time at 14-12.
But Care's charged-down kick immediately put them on the back foot again, Cipriani scrambling back to avert a potential Australian try after Nathan Sharpe's punt ahead to the line.
The change in scrum fortunes was illustrated when prop Al Baxter, a victim against England in the past, won a penalty from Sheridan at the set-piece, which Giteau landed to regain the lead.
His sixth successful kick at goal swiftly followed, and when Mortlock's monster penalty from just inside the England half drifted over in the 65th minute, Australia were in command at 21-14 up.
A welter of England replacements had arrived either side of the hour mark to try to stem the green-and-gold tide.
But the Wallabies effectively sealed victory 12 minutes from time when Giteau, Ryan Cross and Mortlock combined to send Ashley-Cooper in for a swallow-dive at the right corner.
Giteau landed the extras from wide out to put the seal on a polished individual performance.
England: D Armitage (London Irish); P Sackey (Wasps), J Noon (Newcastle), R Flutey (Wasps), U Monye (Harlequins); D Cipriani (Wasps), D Care (Harlequins); A Sheridan (Sale Sharks), L Mears (Bath), P Vickery (Wasps), S Borthwick (Saracens, capt), T Palmer (Wasps), T Croft (Leicester), T Rees (Wasps), N Easter (Harlequins). Replacements: M Stevens (Bath - for Sheridan 33-40, for Vickery, 54, Vickery for Sheridan, 67), J Haskell (Wasps - for Easter, 59), S Shaw (Wasps - for Palmer 65), M Lipman (Bath - for Rees, 65), H Ellis (Leicester - for Care (67), D Hartley (Northampton - for Mears, 70), T Flood (Leicester - for Cipriani, 72).
Australia: A Ashley-Cooper (ACT Brumbies); P Hynes (Queensland Reds), R Cross (Western Force), S Mortlock (ACT Brumbies, capt), D Mitchell (Western Force); M Giteau (Western Force), L Burgess (NSW Waratahs); B Robinson (NSW Waratahs), S Moore (Queensland Reds), A Baxter (NSW Waratahs), M Chisholm (ACT Brumbies), N Sharpe (Western Force), H McMeniman (Queensland Reds), G Smith (ACT Brumbies), R Brown (Western Force). Replacements: W Palu (NSW Waratahs - for Brown, 45), D Mumm (NSW Waratahs - for Chisholm, 65), T Polota-Nau (NSW Waratahs - for McMeniman, 80). Not Used: M Dunning (NSW Waratahs), S Cordingley (Queensland Reds), Q Cooper (Queensland Reds), D Ioane (Queensland Reds).
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