Wilson, who came third at the Diamond League meeting in Doha earlier this month behind Semenya and Niyonsaba, cruised to victory in a relatively slow time of 2:00.87, with Habitam Alemu of Ethiopia in second and Nelly Jepkosgei of Kenya in third.
Double Olympic champion Semenya and Niyonsaba share a string of Diamond League victories in the distance going back over three years, but both are no longer allowed to compete without taking medication to reduce their testosterone levels.
The IAAF, Athletics' governing body, has imposed the conditions on female athletes with differences in sexual development (DSDs). Semenya has filed an appeal against the rules to Switzerland's highest court.
Earlier in the evening Michael Norman, whose time of 43.45 in Torrence, California last month is the fastest 400 metres in the world this year, held off a strong early challenge from compatriot Rai Benjamin to win in a time of 44.53 in tough conditions.
The women's 200m provided the other highlight of the evening as European Champion Dina Asher-Smith emerged early from a strong field to take the win in a time 22:18, ahead of double Olympic champion Elaine Thompson of Jamaica and decorated Dutch sprinter Dafne Schippers.
"I just wanted to come and secure the win, but to secure a fast time too, I'm not going to complain," an elated Asher-Smith said following her blistering performance.
The much-anticipated debut of Kenya's Hellen Obiri in the women’s 5000 metres ended in disappointment as she fell around the four-kilometre mark of the race while battling for third spot.
A gold medallist at the IAAF World Cross Country Championships in March, Obiri scored an impressive victory over 3000 metres in Doha but finished second-last after her slip, with Agnes Tirop winning in a time of 14:50.82.
The men's 1500 rounded off the night with Timothy Cheruiyot blasting to victory in time of 3:35.79 ahead of Ayanleh Souleiman of Djibouti and Norway's Jakob Ingebrigtsen.
The Swedish crowd had little to cheer until late in the evening when Daniel Staahl secured victory in the discus 69.57, his second Diamond League win of the season.
(This version of the story refiles to fix day in intro.)
(Reporting by Philip O'Connor; Editing by Toby Davis)
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