Until the announcement, Pinto had been economic advisor to the outgoing Uribe government.
The head of state made the announcement by means of a presidential decree, that came into effect on Friday, July 31.
Pearl, a former economist, had occupied the post of high commissioner for peace since February 5, 2009. He has also given up his role as high commissioner for social and economic reintegration of armed persons and groups, a post which he had held since 2006.
Pearl is thought to be planning to return to academia and business.
As yet no reason has been given for his resignation.