The Jamaican, who retained her 100m-200m title double in Tokyo, clocked a new world lead of 10.54 seconds.
Only American Florence Griffith-Joyner has run faster, when she set her world record of 10.49 secs in 1988.
Britain’s Dina Asher-Smith finished third in the 200m as she continues her return from the hamstring injury that blighted her Olympic campaign.
The race was won by Switzerland’s Mujinga Kambundji, with American Gabrielle Thomas finishing 0.08 secs ahead of world champion Asher-Smith.
In the 100m, Thompson-Herah’s Jamaican compatriots Shelly-Ann Fraser-Pryce and Shericka Jackson were second and third respectively in a repeat of the Tokyo podium.
American Sha’Carri Richardson, who missed the Olympics because of a one-month suspension after testing positive for marijuana, finished last.
“It was a great return back to the sport,” the 21-year-old said. “I wanted to be able to come and perform. Having the month off, dealing with all I had to deal with, I’m not upset with myself at all.
“This is one race, I’m not done. You know what I’m capable of. Count me out if you want to, because I’m here to stay.”
Earlier this season, Fraser-Pryce ran 10.63 secs to become the second fastest woman in history behind Griffith-Joyner, only to see her time usurped by 29-year-old Thompson-Herah with 10.61 secs as she retained her Olympic title in Tokyo.
Records tumbled in all corners of the Prefontaine Classic in Eugene, with Olympic medallists continuing their fine form back on the Diamond League tour.
Tokyo bronze medallist Andre de Grasse won the men’s 100m in 9.74 secs, with Americans Fred Kerley – the Olympic silver medal winner – and Ronnie Baker crossing the line in second and third.
In the men’s 200m, American Olympic bronze medallist Noah Lyles set a new meeting record and world lead of 19.52 secs.
Athing Mu followed up her women’s 800m gold in Tokyo with victory in the non-Diamond League event in Eugene, setting a new world lead of one minute 55.04 secs in a race that saw Britain’s Olympic silver medallist Keely Hodgkinson place fifth and Jemma Reekie eighth.
Norway’s Olympic 1500m champion Jakob Ingebrigtsen was victorious over one mile in a new world leading time of three minutes 47.24 secs, while two-time Olympic champion Faith Kipyegon of Kenya won the 1500m, with Laura Muir, who won silver in Tokyo, only managing 12th.
Olympic silver medallist Dalilah Muhammad set a new meeting record of 52.77 secs in the 400m hurdles, while Kenya’s Norah Jeruto won the women’s 3,000m steeplechase and Uganda’s 5,000m gold medallist Joshua Cheptegei set a new two-mile world lead of eight minutes 9.55 secs.
In the field events, Olympic pole vault champion Katie Nageotte, also of the US, won with a jump of 4.82m, again finishing ahead of Tokyo silver medallist Holly Bradshaw.
Portugal’s triple jump Olympic champion Pedro Pichardo continued his winning form at Hayward Field, while Ukraine’s Iryna Gerashchenko, fourth in Tokyo, won the women’s high jump.
Two-time Olympic shot put champion Ryan Crouser of the US set a new Diamond League record of 23.15m
Elsewhere, Elliot Giles finished fourth in the men’s 800m – won by Canada’s Marco Arop – while British team-mate Oliver Dustin slipped down into seventh after leading into the final straight.
Next stop on the Diamond League tour is Lausanne on Thursday, before Paris next Saturday.