The 32-year-old Sebrle completed his collection of gold medals when he captured the only major event to have eluded him with a total of 8,676 points, 350 points less than the world record he set in 2001.
Maurice Smith of Jamaica finished second with 8,644 points after leading for most of the two-day competition and Dmitriy Karpov of Kazakhstan was third with 8,586 points, adding a second bronze medal to his podium finish in 2003.
Sebrle won the Olympic title at Athens in 2004 and had twice won the European and world indoor crown but the outdoor world had escaped his grasp.
"This is the toughest of all my titles and very emotional," Sebrle told a news conference.
"Now I have a full collection of medals and titles but my motivation still remains. I need to defend my title from Athens next year."
Sebrle finished second behind Tom Pappas at the 2003 world championships in Paris and was runner-up
Clay withdrew on Friday when he pulled a quadricep muscle during the high jump and Pappas pulled out on Saturday with a foot injury.
Sebrle was in third place behind Smith and Karpov after the first day but soared past both men to snatch the outright lead after the penultimate event, the javelin, with a mighty throw of 71.18 metres.
"That was a crazy competition with so many ups and downs," Sebrle said. "It just proved that decathlon is not finished until after the last event."
Smith, whose 32-point loss was the closest margin in a world championship decathlon, finished the final event, the 1,500m, just ahead of Sebrle but not enough to win the gold.
"I really surprised myself with the overall result, I feel like a winner," Smith said.
"I feel so proud of my performance. I came here to Osaka prepared to win a medal and I expected Roman to win the gold."