That wrapped up a 4-0 aggregate win and Bayern were rarely in danger of letting their lead slip.
Mario Mandzukic headed home in the second half and Claudio Pizarro netted another in the dying seconds.
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Since Guus Hiddink arrived at the helm, Chelsea have improved considerably after a tricky start to the campaign.
Newcastle United are staring down the barrel of relegation to the Championship for the second time in the past eight years.