He edged out local favourite Su Bingtian (10.05), while China's Xie Zhenye came third in 10.17 and Gatlin trailed in seventh (10.20).
Lyu HuiHui of China, the World Championships bronze medallist in London past year, won with a meeting record of 66.85m in the third round.
Su said he was satisfied with this result: "It is beyond my expectation, I felt a little nervous when it rained, but then felt good in the whole race, just a little tough in the last 30 meters". "It is definitely the happiest moment in my time on the Diamond League circuit".
The Dutch sprinter clocked 22.34 for second place ahead of Jamaica's Shericka Jackson, who recorded 22.36, with world silver medallist Marie-Joe Ta Lou of the Ivory Coast fourth in 22.38. Miller-Uibo Shaunae from Bahamas stormed to win the women's 200 meters with 22.06 seconds while Brianna Mcneal of United States beat her teammate Sharika Nelvis to win the women's 100m hurdles.
That was one of five meeting records broken, while there were also eight world leads set at the Shanghai stadium.
Manyonga took the lead in the fourth round, leaping the same distance as Chinese athlete Shi Yuhao (8.43m), but he went on to cement the victory with a Season's Best of 8.56m in round six - which was the best jump in the world this year.
Meanwhile, reigning world champion Gong Lijiao of China hurled a season best of 19.99 metres for all women shot putters to win here.
Jamaican Omar McLeod won in his first 110m hurdles race since adding the 2017 World title to his Olympic gold.
Olympic champion Dalilah Muhammad held off Jamaican Janieve Russell by.01 in the 400m hurdles, clocking 53.77.
Beatrice Chepkoech of Kenya won the women's 3000m steeplechase in 9:07.27, the fastest time this year.
The men's 800m produced a breakthrough victory for another young Kenyan, Wycliffe Kinyamal, in a meeting record of 1:43.91.
Though some of the world's top two-lap stars are giving the event a miss, Van Rensburg will line up against a handful of worthy opponents including Polish athlete Marcin Lewandowski and two-time world indoor championships medallist Andrew Osagie of Great Britain.
Kenya's world 1500m silver medallist Timothy Cheruyiot was a victor of the 1,500m in 3:31.48, a 2018 leading time, ahead of Ethiopia's Samuel Tefera, who set a personal best of 3:31.63.
American Paul Chelimo fell at the finish line in a failed attempt to win his first worldwide race in a deep 5000m.
Colombia's Olympic gold medallist Caterine Ibarguen easily won the women's triple jump with 14.80 metres.
Russia's Maria Lasitskene cleared a world-leading 1.97m to win the high jump, while France's Renaud Lavillenie won the pole vault on countback ahead of Poland's Piotr Lisek, as both athletes cleared 5.81m.