Brunne, 55, is in a registered partnership with the Rev. Gunilla Lindén and they have a 3-year-old son.
Brunne received 413 votes against 365 for her challenger, the Rev. Hans Ulfvebrand. The electors are clergy members and an equal number of lay people.
Brunne is believed to be the first openly lesbian bishop in the world.
The Church of Sweden is Lutheran and counts 76 percent of the population as members, although only about 2 percent of them regularly attend services.