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VIDEO: Frank Lampard's 'goal'
Klose and Podolski put the Germans in command with poachers' goals after 20 and 32 minutes with England's defence all at sea.
But Upson headed in eight minutes before the interval and England should have gone in level after a Frank Lampard shot crossed the line coming down off the underside of the crossbar, only for the linesman to wave play on.
Mueller's second-half double finished off a woeful England.
Three-times champions Germany, whose speed and guile frequently bewildered a statuesque England backline, will now meet either Argentina or Mexico, who were facing off later on Sunday in Johannesburg.
Germany, a youthful side just coming to the boil under coach Joachim Loew, continue their record of having reached at least the last eight in every World Cup they have competed in since 1938.
England, having come to the tournament with high expectations under experienced coach Fabio Capello, in contrast will head home with their reputations in shreds ahead of the customarily savage media post-mortem.
