Blake outran the Olympic champion by 0.11 seconds Friday, streaking across the finish line in Jamaica in a time of 9.75 seconds.
"It's awesome," said Blake. "I won the world championship, so I've got that. Now, I'm the national champion for Jamaica, so I've got that. And now, I go into the Olympics like this."
Former world-record holder Asafa Powell was third, guaranteeing Jamaica an imposing team for the marquee event at the upcoming London Olympics.
Blake's winning time was just 0.01 seconds faster than Bolt's best time of the year. But Bolt got off to a relatively slow start and had to close strong to get past Powell and grab second place, Britain's The Daily Telegraph said.