Shops and schools throughout Indian-administered Kashmir remained closed on Friday in protest at the suspected killing of a leading militant.
Police say Saif-ul-Islam was killed during a gun-battle between militants and Indian security forces.
Thousands are protesting Saif-ul-Islam's death
His supporters organised the general strike and asked for people to offer special prayers.
There have been calls for an independent inquiry after it was alleged that his throat had been slit and his body showed signs of torture.
Saif-ul-Islam was the chief commander of the Pakistan-based Hizbul Mujahideen, one of the biggest militant groups operating in Indian-administered Kashmir.
The response to the strike call was near total with normal life in Saif-ul-Islam's home town coming to a standstill shortly after his death on Wednesday.
The call for an inquiry into Saif-ul-Islam's death was made on Thursday by the Jammu and Kashmir High Court Bar Association.
It described his death as a "custodial killing" and a flagrant violation of human rights.
The association is boycotting courts in Kashmir on Friday in protest at the death.
Indian police and paramilitary forces say they arrested Saif-ul-Islam on Wednesday.
They say he then led them to a hideout to find hidden arms supplies but was killed after militants hiding there exchanged fire with the security forces.
Saif-ul-Islam was the second in command to Hizbul Mujahideen leader Syed Salahuddin and one of the founder members of the group, when it was launched in late 1989 in Indian-administered Kashmir
Hizbul Mujahideen have now appointed a new chief of operations and vowed that struggle would continue.
In a statement by the separatist group, it was announced that Ghazi Nasir-ud-Din had been unanimously appointed by the council to replace Siaf-ul-Islam.
A spokesman for the separatist group, Salim Hashmi, said the command council paid tribute to Saif-ul-Islam and added that they would continue the holy war "until there is freedom for Kashmir".
Syed Salahuddin told the BBC that the death of Saif-ul-Islam "would not adversely affect" the separatist movement.
He added that his death would generate a new sense of energy within the organisation.
Saif-ul-Islam took over as the commander of the group's Indian operations replacing Abdul Majid Dar who was expelled from the group last year.
Mr Dar had announced a unilateral ceasefire with the Indians three years ago, a move that was opposed by Mr Salahuddin.
Last month, unidentified gunmen killed Mr Dar in his hometown, Sopore.
That shooting has led to tensions between two factions of the Hizbul Mujahideen.
On Tuesday, police in Muzaffarabad arrested more than a dozen members of the two factions to avert a possible clash.