Judge Chaudhry Habib-ur-Rehman exonerated Aziz and the others, including his relatives and colleagues for the murder of paramilitary Pakistan Rangers official.
The murder case was registered after the army conducted an operation against extremists holed up in the Lal Masjid in Islamabad in 2007.
"Today, Allah has awarded us with another success and the court's verdict has proved that (former President) Pervez Musharraf's allegations were wrong," Aziz told the media outside the court.
The court had earlier issued arrest warrants for four of the accused in the case, including former intelligence official Khalid Khwaja, who was kidnapped and killed by militants in northwest Pakistan.
Abdul Rashid Ghazi, the brother of Abdul Aziz, was among some 100 people who were killed during the operation against the extremists in Lal Masjid.
Abdul Aziz was caught by security personnel trying to sneak out of the mosque wearing a burqa.
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He has been acquitted in 18 of the 27 cases registered against him.
He was freed from house arrest in 2009 and is back at the Lal Masjid leading prayers.