The tri-series will start from July 26 with the final taking place on August 8.
"Afghanistan were deservedly granted full member status at the ICC annual conference last month after showing impressive growth in recent years", CSA chief executive Haroon Lorgat said.
Afghanistan will now join South Africa and India for the series starting later this month.
Now, with the Afghanistan Cricket Board accepting CSA's invitation, the tri-series will progress as planned, with the first match slated for July 26 between Afghanistan and India in Pretoria.
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Afghanistan was recently given an entry into Test Cricket.
Last month, the International Cricket Council (ICC) granted test status to two nations, Afghanistan and Ireland.
India A is the third side in the triangular series. "This will be our first-ever visit to South Africa and I am certain that this will give Afghanistan "A" team very good exposure to competitive cricket". It will be a great opportunity for the Afghan boys to play against two of the stronger teams in global circuit. The tri-series would be followed by two four-day games between India "A" and South Africa "A" scheduled for August 12 in Benoni and August 19 in Potchefstroom.
The giant strides that they have made in global cricket, a just reward for which was the exhibition game against MCC XI at Lord's, demand more opportunities so that the players get to play against stop-quality sides and gain exposure.