Haq Nawaz was hanged early on Wednesday morning at Mainwali jail in Punjab province amid intense security preparations.
Haq Nawaz was hanged early on Wednesday morning at Mainwali jail in Punjab province amid intense security preparations.
His body was later released to relatives for burial.
The execution led to clashes between police and protesters in Nawaz's hometown, in which one person was killed.
Security fears
Several hundred supporters of the militant group Nawaz belonged to, Sepa-e-Sahaba, had been taken into custody before the execution to prevent large-scale protests.
Security throughout Pakistan was tightened ahead of the hanging.
But after the execution, a confrontation developed in the town of Jhang in Punjab province where Nawaz was due to be buried.
Police said they had used bullets and teargas after coming under attack from his supporters who had assembled outside Nawaz's house.
One person was killed and six others were wounded - although members of Sepa-e-Sahaba said the number of wounded was higher.
Nawaz was sentenced to death by an anti-terrorism court 10 years ago after being found guilty of shooting Sadiq Ganji, who was the Director of the Iranian Cultural Centre in the Punjab capital, Lahore.
Mr Ganji was the first prominent Shi'a Muslim from Iran to be killed in violence between Shi'as and Sunnis which began around two decades ago and has so far resulted in around 1,000 deaths.
Since then, several Iranian Shi'as have been murdered in sectarian attacks that have been blamed on the hard-line Sunni Sepa-e-Sahaba organisation.
The violence has at times severely strained Islamabad's relations with Tehran.
Sectarian violence
Mr Nawaz was one of the first Sepa-e-Sahaba members to face the gallows.
The military government refused to commute his sentence, stressing that it was determined to prevent what it says are extremist groups from wielding too much influence in Pakistan.
The government says that its in a better position to clamp down on sectarian violence than its civilian predecessors, who it argues were often held to ransom by hard-line groups.
Meanwhile, the sectarian violence which has dogged Pakistan for much of the last 10 years has continued unabated: in just over a week, seven people, six of them Shi'as, have been killed.