Van Zyl finished fourth, clocking 49.07 seconds for his slowest performance of the year.
Puerto Rican Javier Culson won the race in a season's best 48.50.
Culson was followed by American Bershawn Jackson (48.55) and Briton David Greene (49.07).
Van Zyl, who won the first two Diamond League races in his discipline in Doha and Rome, remains the only one-lap hurdler to run below 48 seconds this season.
He also leads the 400m hurdles Diamond League race with eight points. Culson is second with four points.
In the men's 800m event, South African world champion Mbulaeni Mulaudzi finished second, clocking 1:46.68.
Mulaudzi took the lead after world-leading Abubaker Kaki of Sudan pulled out with an injury 300 metres in to the race.
The South African held on until Alfred Kirwa Yego of Kenya, who won in 1:46.57, passed him in the final stretch.
Yego's compatriot, Kiplagat Lalang, finished hot on Mulaudzi's heels in 1:46.75.
South African women's javelin throw record holder Sunette Viljoen finished second, with a best heave of 60.39.
Christina Obergfoll of Germany won with a 64.43m meeting record to stretch her lead in the Diamond race.
Double amputee Oscar Pistorius once again failed to qualify for the World Championships in the men's 400m after finishing fifth in 45.69.
South African junior record holder Cheyne Rahme failed to clear a height in the men's pole vault on his Diamond League debut.
Rahme skipped the first height of 5.22m and failed with three attempts over 5.42m.