(BBC) The American overhauled Asafa Powell in the final 30m to edge out the Jamaican by one hundredth of a second.
Olympic champion Usain Bolt opened his 2012 campaign with a run of 9.82 seconds in Kingston on 5 May.
Gatlin, who won 100m gold at Athens 2004, is eligible for London 2012 after serving a four-year doping ban.
His victory at the Qatar Sports Club marked a return to the venue where he set a new world record in 2006, a mark subsequently wiped from the record books after testing positive for testosterone.
The 30-year-old made his comeback to athletics in 2010 and won 60m gold ahead of Great Britain's Dwain Chambers at the Indoor World Championships in Istanbul in March.
Whether Gatlin gets a chance to compete for a medal at the Olympic Stadium in August is dependent on his performance in the United States trials in Portland which begin on 21 June.
Regardless of his presence, a cast of credible pretenders to Bolt's crown have made their case.
With Commonwealth champion Lerone Clarke finishing third behind Gatlin and Powell in 9.99 seconds, six men have run under 10 seconds already this season.
American Walter Dix, who won bronze in both the 100m and 200m behind Bolt at the Beijing Games, won the event's 200m in 20.02 seconds.
In a field packed with quality, American three-time world champion Allyson Felix trumped the challenge of her Jamaican rivals to win the women's 100m in 10.91 seconds.
Veronica Campbell-Brown and Shelly-Ann Fraser-Pryce, Olympic champions at 200m and 100m respectively, finished second and third.
Elsewhere in the season's opening elite-level Diamond League meeting, Great Britain's Perri Shakes-Drayton came third in the women's 400m hurdles in a time of 55.25 seconds, behind Jamaica's Olympic champion Melaine Walker in 54.63.
Her compatriot Martyn Rooney finished fourth in the men's 400m in 44.99 seconds, eight tenths of a second off Olympic champion Lashawn Merritt.
Greg Rutherford, who has 2012's world-leading jump at 8.35m, came a disappointing fourth in the men's long jump with a leap of 7.98m behind Russia's Aleksandr Menkov.
But fellow Briton Andrew Osagie ran a personal best of one minute, 44.64 seconds as he finished third in the men's 800m behind Kenyan winner David Rudisha, while Molly Beckwith racked up a season's best of 1:59.51 as she came home sixth in the women's 800m.
Kate Dennison was fourth in the pole vault after clearing 4.50m, while Vivian Cheruiyot beat Meseret Defar in the women's 3,000m.
Friday, May 11, 2012
3:49 PM dhm