The 24-year-old American beat the previous mark of 9.77 set by Jamaica's Asafa Powell in Athens on June 14.
"I am the best of the best because I am the Olympic champion, the world champion and the world record holder now," Gatlin told reporters.
"I thought I would do it and I kept my word. I am a man who likes challenges and my acceleration today was phenomenal."
Gatlin announced he had his sights set on the world record earlier this week after clocking 9.95 seconds in his first outing of the season in Osaka last Saturday.
He recorded the fastest time in the world this year, 9.85 seconds, in the Doha semi-final.
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The pair last met on the track in London in July when Powell pulled up with a groin problem that put paid to his season.
Gatlin said the world record could go again later in 2006.
"The timings could be further improved this year, probably in Europe," said Gatlin, who dedicated his record to God and his parents.
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