The sixth-seeded Spaniards claimed their first win over the American twins in their fourth attempt, preventing the Bryans from claiming a fourth title at the year-end elite tournament.
It is the second year in a row that a Spanish duo won the doubles in London. Marcel Granollers and Marc Lopez won last season.
The Bryans have finished No. 1 for a fifth straight year and a record ninth time overall. They have won 11 titles this season, including the Australian Open, French Open and Wimbledon.