As low clouds settled around the stadium for the evening meet, the Jamaican sprinter pulled away from her American rival to clock 10.93 seconds, the fastest time of the year.
"I just came out to execute a good race, and I think I did that," Fraser-Pryce told reporters. "I'm just looking forward to the rest of the season. I pray to God that if I can continue to stay healthy, that is key at this moment because it's a long season."
Jeter, who needed treatment for a leg injury, told stadium officials that it was too early to know the extent of her injury.
In the men's 400 metres London gold medalist Kirani James eased away from American rival Lashawn Merritt down the home straight.
"It was good, I had Lashawn in front of me. And so he really set the pace and it kind of prepared me to put on a good performance," said the Grenadian sprinter.
It was the first time the two rivals have met since Merritt was forced to pull out last year's London Olympics.
"It's my first 400, my opener and I've got a lot more training to put in. I've been training hard, came out and ran a healthy race," said Merritt. "Is he unbeatable? Not at all. Everybody's beatable. Next race I'll come more prepared and we'll go at it again."
WEIR PIPS GATLIN
Chinese sprint hope Zhang Peimeng broke the national 200 metres record just weeks after he ran China's fastest 100 metres, but failed to trouble the leaders as Olympic bronze medalist Warren Weir pipped American rival Justin Gatlin.
"It's not a surprise for me to break the national record since I have already proved myself in the 100. I feel I still have room to improve and I can do better next time," Zhang said.
In the 110 metre hurdles, London silver medalist Jason Richardson won in 13.23 seconds after his fellow-American Aries Merritt sustained an injury in the warmup.
"I felt a cramp in my hamstring and I didn't want to risk it. I didn't want to pull my hamstring and be done for the season," said Olympic champion and world record holder Merritt.
Richardson said he was concentrating on the Moscow world championships in August.
"I'm thinking about Moscow every day to defend my world championship title. I just need to make sure I peak in August," he said.
In the absence of high hurdler Liu Xiang, a number of local athletes put in strong performances, with Li Jinzhe leading the field in the long jump and Xie Wenjun coming third in the 110 metre hurdles.
Ethiopian Genzebe Dibaba outpaced Olympic champion and compatriot Meseret Defar in the women's 5,000 metres. Defar snatched Olympic gold in London from Genzebe's sister Tirunesh.
Russian world record holder Yelena Isinbayeva won the women's pole vault with a mark of 4.70, before falling short on two attempts to reach 4.85.
"There's no point in just jumping 10 centimetres higher," she said. "I was confident if there was no pain then I could jump higher than 4.85 and maybe 4.90."
Meanwhile, British golden boy Greg Rutherford, who took gold in the long jump at the London Olympics had to settle for third behind China's Li Jinzhe's world leading distance of 8.34 metres.
"I go to every competition to win it, that's why I'm disappointed to finish third today. Going forward, by the time Moscow comes around I expect to be in very good shape and hopefully able to jump a lot further than last year," Rutherford he said.