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Image from Puella Magi Madoka Magica the Movie: Beginnings - 49m29s
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The roof of the cathedral. Unfortunately there were renovations going on when I visited, but you can see the spires and the structure in the middle of the shot that matches.
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Image from Puella Magi Madoka Magica the Movie: Rebellion - 12m42s
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Closer look from the third movie.
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Image from Puella Magi Madoka Magica the Movie: Rebellion - 12m35s
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In the movies they have the structure in the middle on both ends on the roof, but there's just one in real life. This is the actual view in the opposite direction.
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It wasn't shown in the movies, but here's a look at the front of the cathedral as well.
No map since this is a famous tourist attraction.
This location was visited on 2018/10/18.
Links:
Cathedral official website