Striker Lukas Podolski rested the whole game and midfielder Thomas Muller entered midway through the second half.
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He boosts their contingent of Germany internationals including Klose, Lukas Podolski, Bastian Schweinsteiger, Jan Schlaudraff and Marcell Jansen.
Olivier Giroud scored twice, while Lukas Podolski, Santi Cazorla and Theo Walcott were also on target for the Gunners.
But Danny Gabbidon epitomised Wales' determination as he put his body on the line once again to block Podolski's goal-bound effort.
Arsenal paid more than double that to sign French striker Olivier Giroud, Spanish midfielder Santi Cazorla and German forward Lukas Podolski.
Cazorla's arrival at Arsenal follows the club's summer signings of Germany forward Lukas Podolski and France international striker Olivier Giroud.
Striker Van Persie was sold to Manchester United, with the likes of Lukas Podolski, Santi Cazorla and Olivier Giroud joining the Gunners.
Podolski, who was born in Poland, and Miroslav Klose, who is half-Polish.
The comeback was completed when Lukas Podolski scored a third in injury time to hand Arsenal their eighth league win in ten games.
The Wolves stopper produced another great save soon after to deny Lukas Podolski from 10 yards, after the Bayern Munich striker was put through by Ballack.
The game was always close to boiling over, and Lukas Podolski went down after an off-the-ball clash with Rene Aufhauser, then went eyeball to eyeball with Emanuel Pogatetz.
England's defenders were caught out of position again for Germany's second goal as Muller shifted the ball to Podolski, who slashed a left-footed shot into the far corner.
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Lukas Podolski, who had been doubtful with a calf injury, burst down the left and sent in a low cross which Schweinsteiger tapped home at the near post.
Podolski then wasted a good chance for Germany when he was put clean through by Thomas Hitzlsperger, only for the Bayern Munich striker to blaze over with just Rustu to beat.
Schwarzer did his best to keep the score down, saving twice from Klose, and once apiece from Sami Khedira and Podolski as Germany tore through the Australia defences time and again.
Loew took the opportunity to rest the likes of Klose, Ozil and Podolski thereafter and, as a result, the Germans were unable to maintain their fluidity in attack in the closing stages.
Lukas Podolski's 78th minute strike earned Arsenal a 1-0 win against Stoke City at the Emirates and close the gap on Everton and fourth-place Tottenham (who play West Bromwich Albion on Sunday) to a point.
Klose silenced the 80, 000-strong Russian home crowd when he stabbed the ball home from six metres after a one-two with Lukas Podolski to score his 50th international goal and set Germany on course for victory in Moscow.
Lukas Podolski and Miroslav Klose continued their remarkable scoring record at international level with a goal apiece to take their joint tally to 88, Thomas Mueller and Cacau added the gloss, while in playmaker Mesut Ozil they appear to have found a real superstar.
Klose has already been denied by Aussie keeper Mark Schwarzer when Podolski drilled in the opener from Mueller's cross, and moments after Klose had wasted another glorious chance, poking wide from eight yards, the Bayern Munich man nodded in Phillip Lahm's delicious cross to make it 2-0.
Whereas some of the last crop of top players decided to play for Germany rather than Poland -- such as Miroslav Klose and Lukas Podolski -- in Borussia Dortmund's striker Robert Lewandowski and captain Jakub "Kuba" Blaszczykowski the country has two players that would grace any team at the Euros.
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