Eighteen days after taking the crown at the World Championships in Moscow, the Jamaican was the slowest of the nine-strong field out of the blocks before coming through to win in 9.90sec.
The world record holder, who branded his start at the London Anniversary Games last month "horrific", had to work all the way to the line, only beginning to pull clear after around 80 metres. Bolt's compatriot Nickel Ashmeade was second in 9.94, with Moscow silver medallist Justin Gatlin third in 9.96.
It was Bolt's first race since competing in Moscow, where he won three golds to take his World Championships medal tally to 10.
"I think the longer the season goes on, the worse my start gets," said Bolt. "The reaction was 0.186, the worst it's been all season. I don't really know what's going on. I'm tired, it's a good thing everyone else is tired too. I'm happy I came out victorious."
Britain's Adam Gemili went within 0.01 of his personal best as he finished eighth in a field which included the top six from the World Championships final and all of whom had gone under 10 seconds before. His time of 10.06 was a season's best.
The 19-year-old became only the second Briton to run under 20 seconds over 200m in Moscow, clocking 19.98 in the semi-final before finishing fifth in the final. It seems only a matter of time before he becomes the first British sprinter to go sub-20 over 200m and sub-10 over 100m.
Bolt said: "He [Gemili] is going to be great, as long as you guys don't pressure him to much. If he's mentally strong he'll do well."
Gemili, too, was unhappy with his start. "I sort of fell out of the blocks and had to pick myself up. I lost maybe a tenth or so. It's great to come into a race like this and feel confident if I execute I can be up there. Hopefully I'll have many more races against him [Bolt] and hopefully I'll get closer and closer."
The best British performance of the night came from Shara Proctor in the long jump. The Anguilla-born athlete beat world champion Brittney Reese, as well as the silver and bronze medallists Blessing Okagbare and Ivana Spanovic, with a leap of 6.88m.