A prosecutor told the BBC that the judge ruled there was insufficient evidence connecting the trio to the 2008 attack that killed six people.
Prosecutor Mohammed Tayyab said Saturday he would ask the Pakistani Supreme Court to reinstate the charges. "We believe our case is very strong and the high court will analyze our evidence again and decide the case in our favor," he said.
The suicide car bombing occurred amid the violent reaction to a Danish newspaper cartoon depicting Islamic prophet Mohammed. Al-Qaida claimed responsibility for the blast, although it was unclear if the defendants had any known ties to the terrorist network.