Bolt was beaten into second place at the Diamond League meeting, 0.01 seconds behind London Games bronze medallist Justin Gatlin who won in 9.94.
Despite a good start, world record holder Bolt looked laboured and was unable to pull away from the field giving Gatlin the chance to edge a thrilling race.
However, the Jamaican appeared unconcerned by the outcome in a news conference spending much of the time shaking his head at a results sheet.
"I didn't feel it (the hamstring) at all during the race. It felt sore after but that was expected. But it isn't a concern for me," said a relaxed Bolt, whose previous outing over the distance was in the Cayman Islands last month where he recorded a relatively pedestrian 10.09.
"I came into this race trying to figure out where I was. Now I need to go back and watch the tape to see where I went wrong and come back better next time.
"I got a great start. My fifth step was kind of bad and I stumbled a bit. The last 50 (metres) I thought would be better. I just need to go home and work out what it is I need to do."
Gatlin by his standards got a slow start but was ahead at halfway and held on for victory.
"It felt good, it's going to be a long season. I'm working on my race strategy and trying to stay healthy," said Gatlin, the 2004 Olympic champion and 2005 double world sprint champion who served a four-year doping ban before returning to athletics in 2010.
"I'm just trying to get my start back and make sure that the middle of my race is good."
The American made it clear, however, that despite the defeat and the injury problems, Bolt would still be the man to beat at August's world championships in Moscow.
"It's an honour to be able to race him and compete against him these last couple of years - he's an inspiration for the sport," said Gatlin "He's brought so much to the sport that wasn't there before.
He's a legend, he's done great things, I just want to go out there and fight to the end."
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- Athletics, Track & Field
- Justin Gatlin