Not in any form that would be useful to a typical tourist. There are a few late night express buses that run from major stations to the outlying suburbs. However, there's no network of buses for routes within central Tokyo.

Your best bet, if you're planning late nights, is to stay close to the entertainment district of your choice. Or suck up the cost of a taxi. Or party on until the first trains (but that can be a more expensive proposition than taking a taxi).

But they're so much more convenient than taxis in other cities (if you're in Tokyo).