Afghan officials earlier said Fazlullah, the chief of Tehrik-e-Taliban Pakistan (TTP) was killed on June 13 when a US spy aircraft fired missiles on his vehicle.
"Yes, we confirm it," Pakistani Foreign Ministry spokesman Mohammad Faisal said at his weekly briefing.
TTP has not yet commented on the death of its leader and Taliban sources say a formal announcement could be made after the militant group elects new leader.
"The killing of the terrorist Mullah Fazlullah, who has been directing terrorism against Pakistan, is a significant development in fighting terrorism," Faisal said.
He said the news of the Taliban leader's death has been received in Pakistan with relief, especially by the families whose loved ones were victims of TTP's terrorist attacks, including the 2014 massacre of an army-run school in the city of Peshawar.
Nearly 150, almost all children, were killed in one of the brutal terrorist attacks in Pakistan.
"Pakistan believes in taking concerted action against terrorism in all its forms. We believe that a cooperative approach would be paramount to defeat the common enemy of terrorism," the spokesman said.
He said Pakistan will continue to hunt TTP militants who are involved in the killing and maiming of innocent Pakistanis.
Pakistani security sources earlier said four guards of Fazlullah were also killed in the drone attack that happened after the Taliban leader visited his militants in Marowara area in Kunar province.
Pakistan insists that Fazlullah had regrouped Pakistani militants in Afghanistan's border regions after they fled to the neighboring countries in recent years.