However, the documents do not provide the same legal status as marriage.
BBC Tokyo correspondent Rupert Wingfield-Hayes says campaigners are welcoming "a small step forward in a deeply conservative country".
Younger people in Japan generally support gay rights but the prime minister has previously urged caution over changing the law.
Hiroko Masuhara, 37, and Koyuki Higashi, 30, were the first to register their partnership in Shibuya district.
Ms Higashi, an actress, told reporters she hoped the measure would spread across Japan and eventually lead to same-sex marriage being legalised.
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