An initial goal from Kingsley Coman in the 8th minute put the team 1-0 up, before Köln's Ljubicic equalized in minute 81.
After a short time under Thomas Tuchel's leadership and a few last minute changes, Jamal Musialia’s 89th minute goal took the win for Munich.
Borussia Dortmund were tipped to win the title initially, but a 2-2 draw with Mainz saw their dreams shattered.
Munich will now face off in a friendly against Manchester City in July, and another with Liverpool in August.
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