Her former husband, Chaudhry Muhammad Shakeel, is accused of murder and is reported to have confessed to strangling her with her scarf.
Chaudhry Muhammad Shahid, her father, is being held as an accessory to her murder.
A lawyer for Samia’s father said he intended to lodge an immediate appeal. At a hearing in the Punjab city of Jhelum, Samia’s uncle and the policeman who headed the original investigation were granted bail.
They were being held on suspicion of falsifying and withholding evidence in the case.
Both men will be released subject to the payment of bonds.
Speaking after the hearing, Mian Muhammad Arif, the lawyer acting for Samia’s father, said he would take the appeal to a higher court in Rawalpindi.
He said the prosecution had failed to come up with any evidence and was basing its case on presumptions.
Ms Shahid, 28, from Bradford, died in July in northern Punjab.
She had been visiting family in the village of Pandori when she died, and her relatives initially said she had suffered a heart attack.
Her second husband, Syed Mukhtar Kazim, believes she was the victim of a so-called honour killing as her family did not approve of their marriage. A post-mortem examination confirmed she died as a result of being strangled.