This episode from the Black Mirror series featured two women in love, Kelly (Gugu Mbatha-Raw) and Yorkie (Mackenzie Davis).
The episode, which had been acclaimed after its airing, thus won the award for Outstanding Television Movie.
Charlie Brooker, who wrote the episode, also won the award for Outstanding Writing for a TV Movie.
At the receipt of the award, Brooker said: "San Junipero was a story about love, and love will defeat hate. Love will win, but it might need a bit of help."
"The Handmaid's Tale" also won several Emmy Awards during the evening including the Emmy Awards for the Best Drama Series.
Actress Elisabeth Moss, who plays the main role, won the Emmy for the best performance in a show.
Season 1 of the series "The Handmaid's Tale" is available on Hulu while waiting for the second season scheduled for 2018.
As for the episode "San Junipero" from Black Mirror, it is available on Netflix.