The Castrol Honda rider ended up fourth in the title race, surrendering his crown to Australia's Troy Corser, who was confirmed as champion when his main rival, Aaron Slight of New Zealand, crashed out of the first contest.
Another Australian, Anthony Gobert, won both races on a Kawasaki, the first by 0.284sec from American Colin Edwards and the second 0.019sec ahead of Slight, Fogarty's team-mate.
Corser, 24, the first Australian to win the title, hoped to cap his success by winning the second race but was thwarted when he hit a seagull on the opening lap. With the front bodywork of his Ducati broken and blood smeared across his helmet visor, he had to return to his pit bay for repairs.
Corser, who amassed 369 points, finished 22 clear of Slight, with John Kocinski of the United States third on 337 and Fogarty fourth with 331.