The two Muttahida Qaumi Movement (MQM) workers, Zubair aka Charya and Abdul Rehman aka Bhola, were sentenced to death by the anti-terrorism court in Karachi which acquitted MQM leader and former home minister Rauf Siddiqui in the same case.
Rauf's lawyer Abid Zaman said the three others were also acquitted by the court.
The court, which has yet to pronounce a detailed verdict, also convicted four gatekeepers of the factory for facilitation.
The Baldia factory fire case has dragged on for seven years and during this period the MQM, which was once a powerful party in Karachi and in the southern Sindh province, has undergone name changes from Muhajir Qaumi Movement to Muttahida Qaumi Movement and also split into several factions.
The fire at the garments' factory in September 2012 killed at least 287 people, according to official figures.
A probe into the fire later revealed that the factory was deliberately set on fire by some MQM workers after its owners refused to pay extortion money to them.
Although some 40 firefighting vehicles tried to control the blaze, hundreds of workers were trapped inside the building which had metal grilles on the windows and no fire exits. Many workers jumped from the upper floors to save their lives.
The judge announced his verdict after some 400 witnesses testified during the high-profile trial in which ten accused were charged with setting the Ali Garments on fire.
They allegedly acted on the instructions of the then chief of MQM's Karachi Tanzeemi Committee Hammad Siddiqui over the non-payment of Rs 250 million 'protection money' by the factory's owners.
Siddiqui and businessman Ali Hasan Qadri were proclaimed offenders in the case as both have reportedly fled abroad and are in hiding.