Germany coach Joachim Loew shrugged: "It was a bad game. We missed the force that we've had over the past few months. It's a day to forget."
Romania became the fourth team to qualify courtesy of their 2-0 win at Luxembourg.
Elsewhere Portugal, hosts of Euro 2004 and beaten finalists, moved into second in Group A thanks to Rooney's Manchester United teammate Cristiano Ronaldo producing the injury time decider in their 2-1 success over Kazakhstan.
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