With just under a month to go before he defends his world 100 and 200 titles in Beijing, the Jamaican showed he had recovered from a pelvic injury that has disrupted his season, although he was left with plenty to ponder in the rain-lashed capital.
The world's fastest man shook off the rust from his layoff - this was his first 100 for over three months and first competitive race since mid-June - to win his heat and the final in the same time, putting him equal sixth in the world this year.
But he had to eat up the ground in the second half of both races, winning the final by three-hundredths of a second ahead of American Mike Rodgers (9.90) and fellow Jamaican Kemar Bailey-Cole (9.92).
"In the final I got a really bad start, I kind of lost focus but I got it back," Bolt told reporters after a routine lap of honour by his own showman standards. "I know I could have gone faster if I had just got my start."
Asked about his fitness, Bolt added: "I'm good. I may go to see the doctor to make sure everything is fine but I'm feeling good. I'm still number one, I've never been number two."
