Bolt shaved 0.03 seconds off his previous fastest time this year -- 9.88 at Monaco in June -- on a warm, still night.
"It was a poor start," said Bolt, the world and Olympic record-holder. "I kind of lost concentration and just went through the line.
"It was OK, I suppose, but I could have done better, especially with the weather like that."
Kim Collins of Saint Kitts and Nevis ran a season-best 10.01 seconds to finish second, ahead of Trinidad's Richard Thompson at 10.03.
With a standing room only crowd at the 61st Boris Hanzekovic Memorial, security had trouble controlling spectators as Bolt celebrated with delirious fans.
"It was wonderful, the crowd here," Bolt said. "I loved that they were excited and that the fans come up to me.
"I'm always grateful for that."
The Jamaican's news conference was cut short when too many journalists tried to force their way into the room.