“We had a meeting with the coach on Monday to discuss the team’s preparations for the world championships in Sydney in August,” Netball SA president Mimi Mthethwa said in a statement on Wednesday.
“At that meeting, she read us a letter tendering her resignation.
“She said she had given the matter much thought and had decided that it was necessary for her to resign.”
Kotze formed part of a coaching panel appointed early in 2011, and was given the sole role in April 2012 after NSA opted to drop the experimental group coaching system.
During her four years at the helm, the Proteas secured historic Test victories over Jamaica and England, but they were unable to secure a medal at a major international championship.
The national federation said it would revert to a group coaching structure to carry the team to the global championships.