Sehitlik Mosque’s two minarets were measured at over 37 metres, 8 more than authorities permitted.
Even the mosque’s dome was 4 metres too high, a costly oversight that needed $90,000 worth of persuasion to stop the city council from demolishing the building.
Stefanie Vogelsang, a municipal official in Neukoelln – a district in the southeast of the capital, expressed her pleasure that the building had been saved.
"I hope that the mosque will contribute to the peaceful co-existence of the various communities in Neukoelln," added Vogelsang.
But there will be no peace soon, there are still plenty of other issues.
For example, the mosque's doors are decorated with ivory and tortoise shell, both of which are tightly restricted in Germany.
Mosque authorities must now prove they obtained the ivory legally.
Nevertheless, the Muslim Central Council believes all problems can be overcome and still plans to open the place of worship before Ramadan, the Muslim month of fast.
The building will have the largest capacity in Germany, holding 2000 worshippers.
But in other German cities, Muslims use warehouses and other buildings as mosques and often these, such as one in Frankfurt, can accommodate far more than 2000.