ECB chief executive David Collier claimed South Africans instigated the exchange, where Pietersen made derogatory comments about his then-captain Andrew Strauss in messages to his rivals.
But the ECB said Monday that "Cricket South Africa has made clear to ECB that the electronic messages were not part of any initiative or plan to undermine the England team or players ... both CSA and ECB regard this matter as now closed."
The ECB, however, said that it still doesn't agree with Cricket South Africa on "the sequence of events regarding any responses to messages between Kevin Pietersen and certain Proteas players."
Meanwhile, Cricket South Africa (CSA) accepted the apology from the English and Wales Cricket Board (ECB) over the infamous SMS exchanges saga that led to Kevin Pietersen's exclusion from the England team.
"CSA has made clear to ECB that the electronic messages were not part of any initiative or plan to undermine the England team or players," CSA said in a statement on Monday.
"ECB has unreservedly accepted that assurance and wishes to reiterate that it has no issue at all with CSA -- or the Proteas players -- on this matter and appreciates that the South African and England players follow the highest ethical standards of behaviour.
"Although the two Boards do not agree on the sequence of events regarding any responses to messages between Kevin Pietersen and certain Proteas players, CSA and SACA accept Mr Collier's apology based upon his earlier utterances that the team may have acted in a way which was underhand."
The statement added that both CSA and ECB now regard this matter as closed and would not comment on the confidential information shared in discussion between the boards.
(With AP and PTI inputs)