Nishiya finished ahead of Brazil's Rayssa Leal -- who at 13 years and 203 days could have become the youngest ever individual Olympic champion -- and Japan's Funa Nakayama, 16.
Nishiya starred in the tricks section to score 15.26 and give the hosts a clean-sweep of the street discipline as skateboarding makes its Olympic debut.
Her performance mirrored that of Japan teammate Yuto Horigome, who won the men's title with a stunning sequence of tricks on Sunday.
US diver Marjorie Gestring remains the youngest individual Olympic champion after winning the 3m springboard at the 1936 Berlin Games at 13 years and 268 days.
Skaters each have two 45-second runs on the equipment and five shots at a one-off trick. Their best four scores out of the seven make up their final total.
Skateboarding is one of four sports making their debut in Tokyo, along with surfing, sport climbing and karate as part of an attempt to bring Olympics to younger audiences
