Bolt, 29, ran 9.81 seconds in his final Olympics to replicate his success at Beijing 2008 and London 2012.
Twice banned for doping offences, Gatlin was 0.08 seconds behind Bolt, with Canada’s Andre de Grasse in third.
“Somebody said I can become immortal,” said Bolt. “Two more medals to go and I can sign off. Immortal.”
De Grasse took bronze in a personal best of 9.91, ahead of Bolt’s Jamaican team-mate Yohan Blake.
Bolt remains on target to leave Rio with a third successive Olympic treble, having won the 100m, 200m and 4x100m relay titles in 2008 and 2012.
He said: “It wasn’t perfect today but I got it done and I’m pretty proud of what I’ve achieved. Nobody else has done it or even attempted it. I expected to go faster, but I’m happy that I won. I did what I had to.”
Bolt was slower out of the blocks than 34-year-old Gatlin, who was aiming to regain the title he won at Athens 2004.
But the Jamaican surged through from 60 metres to pass Gatlin and comfortably win his seventh Olympic gold.
Bolt received a hero’s reception as he walked out into Rio’s Olympic Stadium before the race – and the crowd chanted his name after his victory, too.
“It wasn’t about the time, it was just about winning the gold and going out on top,” said Michael Johnson, four-time Olympic champion.
Bolt, who said in February he would retire from athletics after the 2017 World Championships, competes in qualifying for the men’s 200 on Tuesday, with the 4x100m relay beginning on Friday.
** Wayde Van Niekerk of South Africa smashed Michael Johnson’s 17-year-old 400m world record in becoming the first winner from lane eight since Eric Liddell in 1924. He finished in 43.03s, compared with the American’s 43.18sec in 1999.
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