"Overall we deserved to win, even if it was a hard fought victory," said Heynckes. "Psychologically it was good that we won.
"We were very well organised before the break and our discipline was great. We were fantastic going forward too. The early goals spurred us on."
Mario Mandzukic (6') and Thomas Müeller (11') struck early for Bayern. Robert Lewandoski netted for Dortmund on 75 minutes, but it was not enough to deny Bayern victory.
Bayern last overcame Dortmund in February 2010 and have been subjected to a period of Dortmund dominance over the past few years.
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