The Jamaican became the first man to win three Olympic golds in the blue riband event, landing his seventh crown overall by recovering from an awful start to blast to victory in 9.81 seconds.
The 29-year-old was down at halfway and had to work harder than expected to overhaul the two-time drug cheat Gatlin, who took silver in 9.89secs, with Canada’s Andre de Grasse winning bronze in 9.91s.
Victory on a warm night at the Olympic Stadium left Bolt a 200m victory and a 4x100m relay success away from completing his mission.
“I am a living legend,” Bolt had declared after retaining his Olympic sprint titles at London 2012. He is now well on his way to a whole new level of greatness.
“Somebody said if I win these three gold medals I would be immortal and I kind of liked it. So I’m going to run with that one,” he said on what the next step up would be.
Bolt admitted his performance in the final was far from perfect and blamed a timetable he branded “ridiculous” and “stupid” for his failure to go quicker, with the short-turnaround after the semi-final leaving little time to recover and go again.
He had maintained ahead of the Games that he was in much better shape than last year. And it showed.
He was in cruise control in his heat on Saturday, upping the ante considerably by no more than cantering to 9.86 in the semi-finals, even managing a grin as he glanced right and left, and looked set to go seriously quick in the final.
That did not materialise - his time was a season’s best yet his slowest winning mark in a global 100m final - but Bolt, whatever the situation, knows how to win.
And the gold was what he came for.
“I’m happy and I’m proud of myself,” he said. “It wasn’t perfect execution, but I’m proud of myself.
“I wanted to set myself apart from everybody else and this is the Olympics, I have to do it.
“I came to this Olympics to win three gold medals, to prove myself again as one of the greats.”
Bolt, competing in his final Olympics, took to the track moments after South African Wayde van Niekerk’s stunning 400m world record of 43.03. The biggest name in the sport was in serious danger of being upstaged. And in truth he was.
But the born showman was never going to let that put him off, racing off on a lap of honour, posing for selfies, including with the medallists from the women’s heptathlon, including Jessica Ennis-Hill, with their medal ceremony having taken place shortly before his final.
Bolt is so often dubbed the saviour of athletics in his battle with Gatlin, who has become the personification, rightly or wrongly, of all that is wrong with the sport.
While huge roars and chants of ‘Bolt, Bolt, Bolt’ greeted the Jamaican, his rival was loudly booed as he walked into the 56,000 capacity arena, which was close to full.
“When people come out here they get enthralled in the excitement, I understand that and there’s a lot of Usain Bolt fans and a lot of Jamaican fans,” said the 34-year-old Gatlin, who won Olympic gold 12 years ago.
“But they don’t know me, they don’t know Justin. And I have the respect of my own competitors in the 100m. I’d like to see everyone have respect in the audience.”
Bolt admitted he had never heard boos like it and said he was “shocked”.