All 16 of the country's international airports were cleared to resume their normal flight schedules, a spokesperson said.
The announcement followed an earlier extension of the air space closure until 8 am Wednesday morning, owing to the cloud of ash seeping from the Icelandic volcano Eyjafjallajökull.
The volcanic ash, which floated over much of northern Europe, has caused the worst civil aviation chaos in Europe's history, forcing the virtual shutdown of air travel for nearly six days.
Despite the chaos, about 800 flights took off and landed in Germany on Tuesday, with authorities giving special permission for lower-altitude flights in which pilots flew visually rather than relying on instruments and stayed in constant contact with air traffic controllers. These "visual" rules strictly limit the number of flights that can be allowed, DFS has said.
The special permits were prioritised for flights picking up German travellers stranded abroad.
Airspace closures were meanwhile lifted in several neighbouring countries.