The South Africans used the friendly as preparation for the upcoming Africa Women's Cup of Nations taking place later this year.
The two sides have met on two previous occasions, with the Dutch defeating South Africa in both encounters in 2016 and 2019.
Desiree Ellis' troops got off to rocky start when Jackie Groenen opened the scoring for the Dutch after 12 minutes with a strike from the edge of the box.
Banyana managed to get back on level terms midway through the first when Spanish-based star Thembi Kgatlana collected a pass from Karabo Dlamini before firing home.
The Dutch then took control in the latter stages of the first half, with Lineth Beerensteyn restoring the lead before Vivianne Miedema made it 3-1 before the break.
South Africa were given some hope after the break when Kgatlana won a penalty after being fouled in the box, however, Noko Matlou failed to capitalise as her spot-kick was saved Sari Van Veenendaal.
While Ellis' charges were unable to add to their tally, the Dutch bagged a fourth goal in the 76th minute through Damaris Egurrola's finish before she completed her brace in second-half stoppage time.