The 32-year-old Jamaican, on the comeback trail after taking time away from the sport to give birth to her son Zyon, clocked 10.74 seconds to beat European champion Dina Asher-Smith into second.
Fraser-Pryce had already impressed when finishing second at the Jamaican trials last month, managing the same time (10.73sec) as winner Elaine Thompson.
She won the 100m gold medals at both the 2008 and 2012 Olympics, before having to settle for bronze behind compatriot Thompson in Rio de Janeiro three years ago.
Fraser-Pryce will be a serious contender for a medal at the 2019 World Championships in Doha in September if she can maintain this kind of form.
Her time was only 0.02secs slower than Marion Jones' 21-year-old meeting record.
Britain's Asher-Smith, 23, ran a season's best time of 10.91sec to beat world silver medallist Marie-Josee Ta Lou (10.93sec) into third.