Although the statement did not address the reason of resignation, Obama said his "thoughts and prayers are with Dave and Holly Petraeus" and wish them "the very best at this difficult time."
Petraeus has resigned after admitting an extramarital affair. He said in a statement that he had submitted the letter of resignation to Obama on Thursday and was accepted Friday afternoon.
"After being married for over 37 years, I showed extremely poor judgment by engaging in an extramarital affair. Such behavior is unacceptable, both as a husband and as the leader of an organization such as ours," he said in the statement. "This afternoon, the president graciously accepted my resignation."
The retired four-star general, who served over 37 years in the U.S. Army, took the office as the Director of CIA in September, 2011. He had overseen all coalition forces in Iraq and led the military campaign in Afghanistan.
Senator Dianne Feinstein, chairperson of the Senate Intelligence Committee, said in a statement that she "wished President Obama had not accepted this resignation" but respected the decision.
"This is an enormous loss for our nation's intelligence community and for our country," she said.
First alpine rail gets midnight maintenance