"I am not worried, I want to get faster in the semi-final and get something more in the final," said Bolt.
Read: Bolt, Gatlin rivalry fast out of the blocks
American Gatlin underlined his dominance of the sprints this season by storming to victory in the sixth heat in 9.83 seconds, the best time of the day at the Bird's Nest stadium.
World record holder Bolt, whose season has been disrupted by joint problems, responded by winning the final heat in 9.96, a time which ranked fifth behind Gatlin, American Trayvon Bromell (9.91), France's Jimmy Vicaut (9.92) and Asafa Powell (9.95).
The Olympic and world champion knows that fast times in heats do not win gold medals, however, and was satisfied with going under 10 seconds to reach the semi-finals, which take place along with the final on Sunday.
"It was okay," said the 29-year-old Jamaican. "The execution was okay too. I still have some adjustments; just have to concentrate on my technique now.
"I know Gatlin was running very easy but that is how it is. I am not worried, I want to get faster in the semi-final and get something more in the final."
With the sport in the midst of a crisis over doping allegations, the blue riband sprint has been billed as a battle for the soul of athletics with Gatlin, who has served two doping bans, cast as the villain.
A few boos tumbled down from the stands as he was announced before his heat but the 33-year-old former Olympic and world champion showed his usual focus to win his heat in style.
"My coach told me to go out there and make sure to qualify, I felt safe after like 50 metres so did not have to push it too much," Gatlin said.
"We are here to do our business. It is not about individuals. It's not basketball or football but we do it for our event, for the 100 metres. We want to show our best."
A measure of the depth of the problem of doping in the sprints came when the first three heats were won by men who have also served or completed suspensions for using banned substances in the last two years.
Former world record holder Powell added to his unmatched collection of sub-10 second runs to win the opening heat, while 2007 world champion Tyson Gay was easing up when he crossed the line to win the second in 10.11. Nigerian-born Qatari Femi Ogunode won the third in 9.99.
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