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.
Earlier on Friday, Bahrain's Salwa Eid Naser made it four women's 400-metre victories from as many Diamond League races this year.
Nigerien Aminatou Seyni pushed her all the way, but Naser won in 49.17sec, smashing the previous Lausanne record of 49.45sec set by Marie-Jose Perec in 1996.
Seyni was a relative unknown just two weeks ago, but has since improved her personal best by an incredible one-and-a-half seconds.
"My race was very good," said the 22-year-old.
There were also wins for Olympic champion Caterine Ibarguen in the women's triple jump and Spain's Orlando Ortega in the men's 110m hurdles.
Six men ran sub-1min 45sec times in a remarkable 800m race won by Commonwealth gold medallist Wycliffe Kinyamal of Kenya.