Searching Google for "Day use hotels in Tokyo" throws up a number of options, including Accor, Hilton, Apa, etc. Jalan has a list (in Japanese) of 97 properties in Tokyo that have day use rates. If your preferred hotel is not listed, perhaps you could try asking.

Love hotels, as LapLap mentioned, are also an option, but not ideal if you want to stay put at the end of your "rest". Fortunately, these days there are plenty of hotels where you tack a half day or so on to either end of an ordinary stay.