The 24-year-old Jamaican, who won the 100 and 200 metres at this month's Rio Olympics, clocked a time of 10.78 seconds, well ahead of second-placed American Jenna Prandini (11.11).
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The race was re-run five minutes after a false start that saw only one runner stop as Thompson and the rest of the field sprinted to the finish only to have to go all the way back.
Djibouti's Ayanleh Souleiman set the fifth fastest time ever to win the men's 1,000 metres in 2:13:49, Olympic 1500 champion Matthew Centrowitz of the U.S. finishing sixth in a tired-looking run.
Rio gold medallist Dalilah Muhammad of the U.S. triumphed in the women's 400 hurdles but men's 110 hurdles champion Omar McLeod (13.12) was pipped by Spain's Orlando Ortega (13.11) who was second behind the Jamaican at the Olympics.
Ethiopia's Genzebe Dibaba put the disappointment of Olympic silver behind her in a slow-paced 3,000, clocking 8:31.84 as she came home 20 metres ahead of second-placed Hellen Obiri of Kenya.
Dibaba, voted world athlete of the year in 2015, has had a difficult season due to a toe injury and the arrest of her coach in June on doping charges.
Kendra Harrison, who set a world record 12.20 seconds in London last month after missing out on U.S. qualification for the Olympics, won the 100 hurdles in 12.42, quicker than the time Brianna Rollins set in Rio last week to take gold. After being jeered by a partisan crowd in Brazil 10 days ago, there was a warm reception for Frenchman Renaud Lavillenie but no success in a pole vault competition won by Sam Kendricks.
The American equalled his personal best with an effort of 5.92 metres. Dethroned double Olympic gold medallist Valerie Adams of New Zealand enjoyed a measure of revenge as she won the shot put with a throw of 19.94 to beat Michelle Carter, the American who sprang a surprise in Rio.
(Reporting by Mark Gleeson; Editing by Tony Jimenez; mark.gleeson@thomsonreuters.com; +27828257807; Reuters Messaging: Reuters Messaging: mark.gleeson.thomsonreuters.com@reuters.net)
