Although sluggish from the blocks, the world record holder separated from the field after 40 metres before cruising across the line with the quarter-finals' joint second fastest time.
The six-time Olympic gold medallist, however, was upset at the amount of time he had to wait before getting to run after a succession of false starts in other races.
"It's just the whole system which bothers me, you know I was out there too long," Bolt told Reuters after warming down.
"They (organisers) just sent everybody out and a whole lot of false starts and I was in the last heat and I kind of got cold so I didn't feel as fluent as I wanted to and that's what I was really annoyed about.
"If I can get through that then I'll be fine."
Nickel Ashmeade, who win the third of the four quarter-finals, was the fastest qualifier in a time of 10.07 seconds. Asafa Powell clocked 10.17, while Yohan Blake and Kemar Bailey-Cole both recorded 10.26.
The semi-finals and final are on Friday.
Two-time Olympic champion Shelly-Ann Fraser-Pryce (11.38), Simone Facey (11.31), Elaine Thompson (11.38) and Veronica Campbell-Brown won their heats in the women's 100 to move into the semi-finals.