The South African, who took on the role in August 2021, is expected to join the French Top 14 club Lyon as assistant coach, as reported at the weekend.
It is understood that Zondagh was contracted to the SRU until the Rugby World Cup and the governing body will now decide whether to appoint a replacement ahead of the tournament which begins in France in September.
A statement from the SRU said: “AB Zondagh has left his position as Scotland assistant coach for family reasons and to pursue opportunities. We wish him all the best and thank him for his contribution since joining in 2021.”
Zondagh, 36, came to Scotland after a successful stint in France with Toulouse where he was part of the coaching team which helped the club win the Champions Cup and Top 14 double in season 2020-21. He had previously worked in his native South African with the Natal-based Sharks in various skills and high performance roles as they won the Currie Cup in 2016 and 2018.
He was appointed Scotland assistant coach 16 months ago, with a remit to focus on attack, succeeding Mike Blair who had left to become head coach of Edinburgh.