Atta Ullah and Muhammad Azam linked with Lashkar-e- Jhangvi (LeJ) outfit that regularly targets minority Shiites were hanged in Central Jail Karachi early this morning.
They were convicted for killing of Dr Ali Raza here in 2001 and given death sentence by an anti-terrorist court in 2004.
Later, their death sentence was upheld by the higher courts and their mercy appeal was rejected by Pakistan's President.
The government ended the self-imposed moratorium after Taliban militants stormed a school in Peshawar in December and killed 150 people, including 136 students.
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Pakistan has suffered from a rising tide of sectarian violence in recent years with extremist Sunni Muslim groups such as the LeJ regularly targeting the minority Shiites.
The latest sectarian attack took place on Friday, when a suicide bomber killed 61 people at a Shiite mosque in the Shikarpur district of the Sindh Province.
It was the deadliest attack targeting Shiites in Pakistan since February 2013, when 89 were killed in a market bombing in Quetta