The Jamaican superstar trailed arch-rival Justin Gatlin, roundly booed by the Rio crowd for his doping past, until the 70 meter mark but then swept past the American, finding time to pat his chest as he crossed the line a meter clear.
Gatlin, the 2004 champion who came into the race with the season's fastest time of 9.80, took second in 9.89. Canada's Andre de Grasse claimed bronze in 9.91 seconds - the same finishing order as in last year's world championships.
Victory took Bolt a step closer to his goal of winning a historic "triple-triple" combination of gold in the 100m, 200m and the 4x100m relay in three consecutive Olympics.
Other than the 2011 world championships, when he was disqualified for a false start, Bolt has won every other global championship individual sprint race since 2008.
That equates to five Olympic golds and seven in the world championships. Throw in two more Olympic and four world championship 4x100m relay golds and the world record in all three events and that is total and utter domination.
"This is what we train for. I told you guys I was going to do it," Bolt, 29, told reporters. "Stay tuned, two more to go.
"Somebody said I can become immortal. Two more medals to go and I can sign off. Immortal."
Already assured of his legend status, Bolt also added to his reputation as sport's number-one crowd pleaser as he took a leisurely circuit of the stadium, posing for pictures and shaking a thousand hands.
If the fans were pleased, it is hard to imagine the relief felt by officials of the IAAF and IOC, who must have been dreading a Gatlin victory.
The American has served two drugs bans, though he denies any deliberate wrongdoing for either, and at 34 was bidding to become the oldest 100m champion.
The Rio fans certainly showed what they thought of him as he was loudly booed as he entered the arena, and Gatlin returned the compliment by being the only finalist not to acknowledge the crowd.
Bolt, in contrast, brought the spectators to a fever pitch of excitement as he strolled in, smiling and waving, to chants of "Bolt, Bolt, Bolt."
"I was surprised," Bolt said. "It is the first time I have come into a stadium and they booed someone. It was shocking."
It was no surprise to see Gatlin, the fastest man in the semi-finals, get his usual explosive start but Bolt, who had looked much smoother out of the blocks in his semi than in Saturday's heats, was where he needed to be.
The race followed the pattern of so many before as he eventually unraveled his long legs to gain maximum pace and though he did not hit the front until later than he might have liked, when he did he shot past Gatlin like a track cyclist coming out of a slipstream in the velodrome.
The time was a long way off his 2009 world record of 9.58 but that was never the issue at stake.
Heats for the 200 start on Tuesday with the final on Thursday.