Bolt cruised to victory in 14.42 seconds, falling short of the world-best mark of 14.35 he set on the streets of Manchester in 2009. Antigua and Barbuda's Daniel Bailey was second, ahead of Bruno Lins of Brazil and Ecuador's Alex Quinones.
After the race held under scorching heat on a four-lane track built on Copacabana beach in the city set to host the 2016 Olympics, Bolt said he was satisfied with his performance.
"It was my first sprint race, definitely a good start for the season," Bolt said. "I'm looking forward to coming down here in 2016."
Bolt celebrated by dancing with a few Brazilian dancers after the run, which was an official event supervised by the IAAF.
He threw his running shoes to the fans, who endured huge lines to try to get near the track to see the Jamaican star up close.
Bolt, the first man to successfully defend the 100 and 200 titles at the London Olympics, was in Rio for four days, visiting social projects and participating in promotional events. He also played a volleying match using feet at the beach on Saturday.
Bolt said he is still "not sure" if he will compete at the London Diamond League meet in late July, but agent Ricky Simms reiterated on Sunday that he is working to ensure the Jamaican returns to England.
"We've had positive negotiations, it will be great for him to go back there a year after everything that happened last year," Simms said. "It's going to be a good event. We've just got a few things to finalize. In the next months, hopefully, we'll find solutions."
The London meet, celebrating a year since the Olympics, would be one of his last competitions before the world championships in Moscow in August.
Earlier Sunday, double-amputee Alan Oliveira of Brazil beat American runner Jerome Singleton at the Copacabana track. Oliveira had been initially expected to race against Oscar Pistorius, who withdrew after being charged with the shooting death of girlfriend Reeva Steenkamp. Oliveira beat the South African in the 200 at the London Paralympics.
"I hope everything is solved, that the truth is told and that all parties solve this. Let's see, let's see how things will unfold," Oliveira said, adding that he would like to see Pistorius competing again. "He's a great athlete inside the track, did what he did for Paralympic sport and I hope he continues to do so."