Thompson, who had a poor start crossed the line in 11.01 seconds, while three-time world champion Fraser-Pryce faded to a season-best 11.09 and Olympic 400m bronze medallist Shericka Jackson came third with career-best 11.13.
The 25-year-old Thompson was pleased with the win after an injury-hit start to the season.
"The start wasn't great, but I knew I had to just don't panic, stay in my lane and just swing to the line and that's what I did," Thompson, the joint fourth-fastest woman of all time with a 10.70, told reporters.
"I have to give thanks to coach Stephen Francis because he's been very patient with me for the last couple of weeks. I remember I couldn't train for the entire week after Eugene (Diamond League), it was very rough."
The 11.09 was Fraser-Pryce's best time in 22 months after returning to competition last month following the birth of her first child in 2017.
"Given everything I'm really pleased and blessed with the outcome and looking forward to the rest of the year," Fraser-Pryce said.
In the absence of former world champion Yohan Blake, Tyquendo Tracey produced a career best 10.07 seconds to win his first national 100m title.
Kenroy Anderson was second in 10.24, while Nesta Carter was third in 10.31.
Blake was disqualified in the semi-finals after running under protest, having been charged with a false start.
World championship semi-finalist Julian Forte pulled up injured around 60 metres into the final.
Earlier, Commonwealth Games gold medallist Janieve Russell led from start to finish to win the 400m hurdles in 54.18, as Olympic finalist Annsert Whyte won the men's equivalent from lane eight in 48.80.
(Editing by John O'Brien)
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