The military court had awarded death sentences to Saad Aziz and four others for their role in the Safoora carnage on May 13, 2015, when eight gunmen boarded a bus carrying the Ismaili passengers and opened fire on them, killing 45 people.
Army chief Gen Qamar Javed Bajwa last week confirmed their death sentences along with three other "hardcore terrorists".
In the appeal filed in the Sindh High Court, Aziz and others said their appeals should also be heard as the military court had acquitted three others accused in the same case.
The SHC was informed last Thursday by authorities that the military court had acquitted three suspects who were set free by military authorities.
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The statement came in a letter produced by Judge Advocate -General (JAG) branch of the army in a matter relating to alleged unlawful detention of suspects.
In the cold-blooded sectarian violence, Kalashnikov- wielding militants donning police uniforms had gunned down 45 Shia Ismaili Muslims - 26 men and 17 women - shooting them in the head near Shafoora Chowrangi in Karachi in May 2015.
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