Gatlin, who served a doping ban between 2006-10 and won silvers behind Bolt at the last two world championships, clocked 9.92 seconds, with teammate Christian Coleman winning silver in 9.94sec.
Bolt suffered a dreadful start yesterday and could only claim bronze in 9.95sec.
"I'm sorry I couldn't end it on a winning note, but I want to thank you for your support," said Bolt, who embraced Gatlin after they streaked through the line with no clear victor immediately apparent.
"It's been a wonderful experience as always."
But Gatlin has form as the last man to beat Bolt over 100m -- by a hundredth of a second in Rome in 2013 -- and at the age of 35, can still produce the goods, something he has in the past ironically credited with his four years of forced exile from the track.
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