Berlin was the capital, so it was too important to give to one country, so it got divided separately from the rest of Germany. It’s also worth noting that these territories were supposed to be temporary administrative regions until Germany had its own government that the UK, US, France and USSR were happy with. The issue is that it took decades to reach that point.

It wasn't split into two, it was split into 4, and later became two.

The allies divided up Germany (and Austria) each into 4 sectors (American, British, French, and Soviet). However, they also decided that Berlin so was important, they they would also split Berlin into 4 sectors as well, despite it being inside of the Soviet sector.

Eventually, the American, British, and French sectors of Germany combined to form a singular West Germany, this included their sectors of Berlin as well. The Soviet Sector, including their part of Berlin, became East Germany.

Note that Vienna was also parted into four sectors. Austria however regained independence as a single country in 1955, before the Eastern bloc started their wall-building frenzy.