Bolt, seeking a 12th world title in his swansong season, found himself fifth halfway into the blue riband event before putting on the afterburners to win his heat in 10.07 seconds.
"I stumbled a bit coming out of blocks, I'm not fond of these blocks," he told the BBC.
"I have to get this together. It's shaky because when I did the warm up it (the blocks) pushed back. It's not what I am used to."
Gatlin, the last man to beat Bolt over 100m -- by a hundredth of a second in Rome in 2013 -- was met with loud booing and jeering when shown on the big screen before his heat and after he streaked through in a winning time of 10.05sec in his heat.
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"It's not the panto season," the stadium announcer pleaded to the packed-out 60,000 seater London Stadium as a bemused-looking Gatlin made a sharp exit from the track.
The 35-year-old Gatlin, who served a four-year ban reduced from eight for doping from 2006-10, will be joined in Saturday's semi-finals by compatriots Christian Coleman, who has this season's fastest time of 9.82sec, and Christopher Belcher.
Japan's Abdul Hakim Sani Brown clocked 10.05sec to win his heat ahead of Blake, while China's Bingtian Su also won to ensure a healthy Asian presence in Saturday's races.
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