Gatlin beat Jamaica's Asafa Powell - who ran 9.94secs - with fellow American Tyson Gay third in 9.98secs.
Former Olympic champion Gatlin, 34, who led from the blocks, heads the Diamond League 100m standings after also winning in Shanghai earlier this month.
Femi Ogunode, fastest man in the world this year, was fifth in 10.02secs.
Great Britain's Laura Weightman came sixth in the women's 1500m.
Weightman, 24, clocked a time of four minutes 03.04 seconds in a race won by Kenya's Faith Kipyegon in 3:56.41.
Britain's Tiffany Porter, 28, finished seventh in the women's 100m hurdles behind winner Kendra Harrison.
American Harrison finished in 12.24secs, a new American record and the second fastest time in the history of the event.
In the women's high jump at the event in Eugene, Britain's Isobel Pooley, 23, finished eighth after clearing 1.88 metres.
Justin Gatlin ran his fastest time of the year to win the 100m at the Prefontaine Classic Diamond League meeting in Oregon in 9.88 seconds.