Boucher is serving South Africa as a head coach since December 2019.
Boucher is performing the role since December 2019. During his stint so far, he guided the Proteas to 11 Test wins, including a 2-1 series win over India at home earlier this year.
“Mr Boucher has decided to resign in order to pursue other opportunities in line with his future career and personal objectives,” CSA said in a statement.
“While Cricket SA greatly regrets that Mr Boucher is unable to see out the term of his contract, it respects his decision and wishes him all the best in his future endeavours.”
The Proteas are also occupying the No. 2 spot on the ICC World Test Championship table. In the white-ball format, South Africa won 12 ODIs and 23 T20Is under Boucher.
His last assignment will be the T20 World Cup 2022 in Australia, where South Africa are slotted alongside Bangladesh, India and Pakistan.
The T20 World Cup is due to be played from October 16 to November 13.
CSA Chief Executive Officer Pholetsi Moseki said: “We would like to thank Mark for the time and effort he has invested in South African cricket as the head coach over the past three years.
“He has helped navigate us through some rough waters following the departures of so many senior players through retirement and has helped lay some strong foundations for the next generation of Proteas.
“We are extremely grateful to him for the work he has done and would like to wish him well with the next chapter of his career.”
Director of Cricket Enoch Nkwe added: “We are deeply saddened by Mark’s decision to leave us but we also understand and respect his wishes. He is a Proteas legend and has done so much for the game in our country, both on the field and over the last three years off it, which we highly appreciate.
“He has built a sound platform for South Africa to flourish in all three formats and I’m sure we will see the results of that at the T20 World Cup next month. He has a settled squad already, one that is growing in confidence, and we look forward to watching them in their important series in India before they head to Australia.”
CSA said it announce Mark Boucher’s successor in due course.
(With PTI inputs)