Manyonga earned victory with a best leap of 8.36m, while Samaai took the runner-up spot with a jump of 8.29m. Former Olympic silver medallist Khotso Mokoena finished sixth with a 7.98m attempt.
Fellow hurdler Antonio Alkana was scratched from the Men's 110m Hurdles race after being banished at the blocks due to a false start.
National champion Pieter Conradie was in fine form in the Men's 400m B race, taking the win in 45.88.
Compatriot Rynardt van Rensburg, competing in the 800m national contest ahead of the main programme, grabbed third spot in a Season Best of 1:45.73.
The seventh of 14 legs in the Diamond League series will be held in Paris, France on July 1.