The Tokyo Metropolitan Government is set to begin issuing partnership certificates to same-sex couples in November.
The Tokyo assembly approved the related ordinance on Wednesday that is aimed at promoting a more inclusive society where certificate holders can receive better services.
Members of an advocacy group held a news conference.
Moda Mamiko, who is raising a child with her partner, said she hopes the new system will help to change society.
A specially appointed professor at Waseda University Robert Campbell, who is openly gay, expressed hope that the partnership certificates be a driving force in helping more people to understand sexual minorities.
Officials will start accepting applications from October 11.