The changes were first proposed in 2002 in the Prime Minister's Strategy Unit review of charity law and regulation.
Advertisements for the posts are expected this week, and the commission could break with tradition by appointing someone outside the civil service.
John Stoker, whose five-year term as Chief Charity Commissioner ends in July, said: "I welcome this announcement, which is right for charities and the Charity Commission.
"I hope that the partnership between the new chair and chief executive will be a driving force to turn proposals for reform of charity law into reality."
Voluntary sector minister Fiona Mactaggart said the change was evidence that demonstrates "that the Government is serious about reforming charity law."
According to the Strategy Unit report, the role of the Charity Commission chair will be to "ensure good corporate governance and the smooth functioning of the enlarged board, and represent the commission in public and at a high level within government and the charitable sector."
The commission has traditionally been headed by a career civil servant.
But the commission's head of communications Antony Robbins said the vacancies would be open to people outside of the civil service and candidates would be in post in July.
Other impending reforms to the commission include increasing the number of charity commissioners from five to nine and the creation of an independent appeals tribunal, which will be introduced in the forthcoming Charities Bill.