Naidoo, who was one of the recipients of the undisclosed bonuses, was seen leaving the board meeting, accompanied by her husband.
"This morning, I tendered my resignation to Cricket SA," Naidoo wrote on Twitter.
She also issued a full statement on social networking site Facebook.
"I have stayed until now firstly to allow the processes to fully investigate me, as I have been implicated, and secondly to passionately promote the good work of CSA through a daunting period for it, and not to leave it in the lurch," Naidoo said in her statement.
"Now that the ministerial committee of inquiry has completed its work, I believe that it is the right time to go. Naturally, I remain available to any forum having jurisdiction and requiring input from me," she said.
Naidoo was the third person to quit the embattled organisation this week after acting president AK Khan and chairman of the risk and auditing committee John Blair resigned on Wednesday.
The fallout was a result of a ministerial inquiry, headed by retired judge Chris Nicholson, who released a report to CSA last week.
Nicholson recommended a complete restructuring of the board and Sports Minister Fikile Mbalula told reporters on Friday that it was a watershed moment in cricket.
"If the board of Cricket South Africa has any moral compass, and understands its fiduciary duties, it must, in its meeting tomorrow, do the right thing," Mbalula said.
"Is it not time for the board to make way for a new leadership that will take Cricket South Africa to a new era of hope and clean governance?"