Clearly ahead of the Jamaican world record holder for much of race, Gatlin’s dream fell apart after one final surge by Bolt and an error by the American.
“I gave the race away the last five metres,” Gatlin, who was bidding to become a world champion 10 years and a doping suspension after his first global title, told reporters.
“I had the momentum to lean forward to keep the momentum going and I leaned a little too fast and got off balance.”
That, and Bolt’s fast finish, produced a one-hundredth of a second victory for the Jamaican in a time of 9.79.
“I’m happy that it came so close and I’m happy to represent my country,” the 33-year-old silver medallist said.
“Win or lose, it was a great race against a great guy.”
Gatlin, heavily criticised after serving two doping bans, had not lost a sprint race in two years, winning 27 consecutive 100 and 200 metres events without facing Bolt.
He also finished second to the Jamaican at the 2013 world championships in Moscow.
With Bolt racing infrequently over the past two years because of injuries, Gatlin had become the world’s dominant sprinter, bringing more attention to his doping past which included a four-year ban in 2006.
He entered the championships with the year’s fastest 100 and 200 metres, clocking 9.74 and 19.57 seconds, both lifetime bests despite his age.
By contrast, Bolt’s fastest 100 in 2015 was 9.87 seconds.
The race was billed as a contest between good and evil with Bolt, who has never failed a doping test, representing the good in the most eagerly anticipated event of the world championships.
Gatlin, however, said the pressure had not got to him.
“I’ve had pressure since 2011,” he said. “It’s not the pressure. It’s just to come out here and run.
“The last five metres, it just wasn’t my day. So I have the 200 and the 4x100m (relay) to represent my country.”
(Editing by Ed Osmond)