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.
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.

The attackers entered the Ambassador Hotel on Maka al-Mukarama street after setting off a car bomb at the gates outside, witnesses said.
Somalia's state news agency said two MPs were killed in the blast, with another four rescued.
The al-Shabab militant group was quick to say it was behind the attack.
The BBC's Somali Service reporter Ibrahim Aden in Mogadishu says the explosion is one of the largest to hit the city and the scale of destruction is huge.
Somalia's state news agency Sonna said at least 50 people were hurt and that the death toll was likely to rise.
It named the dead MPs as Abdullahi Jama Kabaweyne and Mohamoud Mohamed Gure.
The head of the city's Amiin ambulance service has told the BBC the main Medina hospital is overcrowded.
"I was the first person to reach scene. The damage was enormous," Dr Abdulkadir Andirahman Haji Aden said.
"My brother and his son were among those injured. We are now in Medina hospital and it is overcrowded with wounded people. I have never seen something like this."
Al-Shabab, which is battling the UN-backed government, was driven from Mogadishu in 2011 but still remains a potent threat and frequently carries out attacks in the city.
The government, with the help of African Union forces, is fighting the al-Qaeda-linked group to regain control of the country.
Earlier on Wednesday, the government announced it had killed Mohamed Kuno, the al-Shabab militant who led the attack on Garissa University in Kenya in April 2015 that killed 148 people.
He was one of 16 al-Shabab militants - four of them senior leaders - killed in an overnight raid on their convoy in Kismayo, a port city in southern Somalia.
A judge in Pakistan has dismissed an application for bail from the father of Samia Shahid, who was allegedly killed in a so-called "honour killing".
[NEXT_CONCEPT]
Gunmen have stormed a hotel in the centre of the Somali capital Mogadishu, with reports of at least 10 dead and 50 wounded.