Most travel agents I know will do this for you, and you can do it for yourself by calling reservations, which will mainly want to make sure you know the airline won't pay for your hotel. I don't think many consumer online res systems can do such a booking, but someone may know better.
It's entirely legit.
Edited to add: I just discovered an airline called "Air Vladivostok" which provides the only service from Vladivostok to Niigata, Japan, and flies just on Thursday and Sunday. Suppose you arrived in Vladivostok on Sunday night after they left, bound for Niigata, could you stay until Thursday without it being a "stopover"? Mostly hypothetical, just curious if any guru knows.
[This message has been edited by RichardInSF (edited 12-20-2002).]