Behind the Jamaican superstar, who took his fourth individual world title, American Justin Gatlin won silver in 9.85 and Bolt’s countryman Nesta Carter took bronze in 9.95.
Briton James Dasaolu, 25, crossed the line in last place after a fantastic start, clocking a slow 10.21 - but will still be pleased to have reached the final.
As rain fell and thunder clapped around the Luzhniki Stadium, a pensive-looking Bolt mimed taking out an umbrella before the start.
Disqualified from the 2011 final for false-starting, Bolt made no mistake out of the blocks this time and although trailing Gatlin - directly to his left - at halfway, he surged to the front at the 60m mark.
Gatlin stayed on his shoulder all the way to the line, followed by Carter and two more Jamaicans, Kemar Bailey-Cole and Nickel Ashmeade.
Bolt said he regretted the weather.
"I wanted to do a better time but was not able to because of the weather," Bolt said. "Not singing in the rain, but running in the rain tonight.
"I'm feeling good, just a little bit tired. I need some rest."
With his world record of 9.58 set at the 2009 Berlin world championships seemingly now a distant memory, Bolt still hammered home the message with each muscle-extending stride that he remains sprint king of the track at 27.
"It was not revenge for Daegu, I just came here to win this title," Bolt added.
"I cannot forget Daegu because all you guys keep reminding me on my false start."
Bolt has been far from his best this season - but his best on the night - the second-fastest time of the year after American Tyson Gay's 9.75 in June - was good enough.
Injured Jamaican Yohan Blake did not defend his title from Daegu, South Korea, while Gay was not in Moscow after testing positive for a banned substance.
That and other positive tests from twice Olympic 200m champion Veronica Campbell-Brown, fellow Jamaican sprinters Asafa Powell and Sherone Simpson and a host of athletes from Turkey and Russia, have dragged down the reputation of the sport.
Bolt, however, is doing all he can to repair.
Former world and Olympic champion Gatlin, twice banned for doping, was disappointed with his performance and not to have won.
"I feel good if I'd run a perfect race and got beaten I would have been concerned, but I didn't run a perfect race," Gatlin said.
"I got a little overexcited and didn't execute the last 30 metres."
World-record holder Bolt regained the title he first won in Berlin in 2009. He will now look to win a seventh and eighth world gold in the 200m and 4x100m relay in Russia.
He also has silver medals in the 200 and relay from the 2007 Worlds in his career haul, along with a perfect six Olympic gold medals from the last two editions of the Games.