Moore, 27, overcame Australia's Nikki Van Dijk in their quarter-final, scoring two excellent 8-point waves combining powerful turns and tube rides to underscore her dominance at Maui's legendary Honolua Bay.
Marks, 17, was knocked out of the contest by Australia's seven-time world champ, Stephanie Gilmore, in their quarter-final. Marks, in only her second year on the top-tier World Championship Tour, had needed to finish at least a couple of places ahead of Moore to overtake her for the world title.
Marks nonetheless qualified for the U.S. Olympic team. She and Moore will represent the United States in surfing's Olympic debut in Tokyo next year, a formidable pairing to take on the likes of Australia and Brazil.
California's Lakey Peterson, who was in second place going into the final event of the 10-stop tour, was knocked out early at Honolua Bay, finishing the year in third and missing out on an Olympics slot.
Only two men and two women per country can qualify for the Olympics team. (Reporting by Lincoln Feast in Sydney; Editing by Cynthia Osterman)