Kumar became chief software architect when he was forced to stand down as CEO earlier this year, following questions over the firm's accountancy practices.
"The board wishes Sanjay and his family well," said chairman of the company Lewis Ranieri. "The board is committed to reaching a settlement of the government's investigation into the company's past accounting practices as quickly as possible. We are working hard to take steps to put this entire matter behind us."
In explaining his decision to leave, Kumar said, "My continued role at CA is not helping the company's efforts to move forward. I believe my decision to leave at this time is the right one. It hopefully will permit CA to move forward."
The United States Attorney's Office is investigating the company.
Ken Cron became acting CEO after Kumar stood down from the role.