Jamaica's Olympic champion and world record holder clocked 10.04 seconds into a head wind to beat Kim Collins of Saint Kitts & Nevis and American Darvis Patton.
It was the slowest time Bolt has run in his 30 sprint finals and a step down from the 9.82 he produced in his only previous outing this season in Kingston, Jamaica on May 5.
He had spoken this week of wanting to run around 9.7 seconds as he continues his build-up to this year's London Games.
"I'm disappointed," Bolt said. "At the start I felt pretty much no energy. I guess it was one of those bad days.
"I wasn't feeling as strong as I usually feel out of the blocks, my legs felt dead. I don't know what the reason is. I'll need to go back to the drawing board, talk to the coach."
Bolt was slow out of the blocks, after South Africa's Simon Magakwe was disqualified for a false start, but easily reeled in Collins, who crossed the line in 10.19 with Patton three one hundredths of a second further back.
The 25-year-old Bolt said the false start did not affect him, yet his reaction time of 0.180 seconds off the line suggested otherwise.
Britain's Dwain Chambers was fifth in a season best 10.28 but failed to reach the Olympic qualifying time of 10.18 that would have guaranteed him eligibility for selection.
Chambers, 34, served a two-year doping ban but was cleared to compete at the London Games when the Court of Arbitration overruled a British Olympic life ban on drug offenders.
In the men's 400 metres, Olympic champion Lashawn Merritt of the United States won in 45.13 seconds while Veronica Campbell-Brown was victorious in the women's 200 in 22.38.
While it was an improvement on the 22.50 Jamaica's twice Olympic champion ran at last week's Shanghai Diamond League meeting, Campbell-Brown's rival, Carmelita Jeter of the United States, still holds the year's quickest time of 22.31.
"I am grateful for the result, the objective is to finish healthy and I am happy I got the victory here tonight," Campbell-Brown said.
"The (Olympic) competition will be tough... it is too early to say (who will be the biggest challenger), there are so many talented women and everybody wants to win. We will get a better idea as we get closer to the Games."
Wallace Spearmon of the United States won the men's 200 in 20.14 while fellow American Sanya Richards-Ross beat Olympic champion Christine Ohuruogu in the women's 400 in 50.65 seconds.
The men's 110 metres hurdles was won by another American, Dexter Faulk, in 13.13, and Briton Tiffany Porter also matched her season best to claim the women's 100 metre hurdles.
Olympic javelin champion Czech Barbora Spotakova overcame her poor record at home meets with a world-leading 67.78 metres with her main rival, Russia's Mariya Abakumova, second (64.34).
"I felt better than ever before at this meeting," Spotakova said. "I had the feeling my best throw was taken down by wind a little, I think I have a few metres left (to improve).
"I am pleased I delivered a balanced series of attempts, that's a good base for one attempt to fly further. And I am happy I beat her," she added, referring to Abakumova.
Vitezslav Vesely capped a great night for the hosts in the javelin by beating Olympic champion Andreas Thorkildsen of Norway with an 85.67 metre effort.