Hingis secured three breaks of serve to Seles' two in a 41-minute first set. At 4-4 in the second, Hingis converted her only break point of the set to pull away from her new doubles partner.
It was Hingis's eighth straight win over world number four Seles.
Seles, who won the trophy with her native Yugoslavia in 1991, is hoping to become the first ever player to win the Hopman Cup twice.
The result left Jan-Michael Gambill needing to beat Roger Federer in the men's singles rubber to keep the U.S. in the tie.
Hingis, 20, and Seles have confirmed they will play women's doubles together at the Sydney International tournament next week and at the Australian Open, which begins on January 15.