Arendse told a press conference here his relationship with Majola had broken down due to "sharply contrasting positions" which threatened to plunge domestic cricket into crisis.
"I never at any stage enjoyed the full trust and confidence of the chief executive and all 11 affiliates, " Arendse said reading from a prepared statement.
The 51-year-old Cape Town-based lawyer claimed six of the CSA affiliates did not back his transformation programme, saying the policy was a "foreign concept" to them.
Majola countered by telling national press agency Sapa he was surprised at the resignation and that "the differences were of management style and hardly irretrievable".
In a bitter clash last February, Majola blocked a move by Arendse to sack national coach Mickey Arthur, who named only four players of colour instead of the planned seven for a tour of Bangladesh.