The 30-year-old claimed victory at the Golden Spike meeting in Ostrava on Wednesday evening, edging out Yunier Perez with a time of 10.06s in the 100m event.
Bolt also clocked 10.03s in Kingston in his last outing earlier this month - the first time in his career that he has been over the 10-second mark in back-to-back races - but the eight-time Olympic gold medallist appeared to be carrying an injury.
Speaking to BBC Sport, he said: "I'm not happy but I'm just getting into my running and have some training to do. I'll be fine. I need to get checked over by my doctor and the coach will give me some training, so no worries."
Bolt is the championships' most successful male athlete, having won 13 medals in all - one fewer than Jamaican compatriot Merlene Ottey, who is the most decorated competitor at the event.