Chaudhry Muhammad Shakeel is accused of murdering the beautician, while her father Chaudhry Muhammad Shahid is being held as an accessory to murder.
The men's lawyers, however, say they will apply to have the case dismissed due to a "complete lack of evidence".
Ms Shahid, 28, from Bradford, died in July in Pakistan.
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Following a court hearing in Jhelum, in the state of Punjab, both men were remanded into custody ahead of their next appearance on 20 October.
The judge ordered that Ms Shahid's second husband Syed Mukhtar Kazim should also appear on that date.
Mr Kazim, who married Ms Shahid in Leeds in 2014 before the couple moved to Dubai in 2015, claims his wife was murdered because her family disapproved of their marriage.
It is thought Ms Shahid had travelled to Pakistan to visit family in the village of Pandori after being told her father was ill.
Her relatives in Pakistan initially said she had suffered a heart attack but a post-mortem examination confirmed she died as a result of being strangled.

Katie Locke, 23, was found dead at Theobolds Park Hotel in Waltham Cross, Hertfordshire. She had been strangled.
Carl Langdell admitted the charge of murder when he appeared at St Albans Crown Court via a video link from Bedford Prison.
A psychiatric report is to be prepared on Langdell who was remanded in custody and will be sentenced on 18 April.
Ann Evans, for the prosecution, said: "What needs to be established are the circumstances of Katie's death. There was a no comment interview with the police."
Benjamin Aina QC, defending, said Langdell admitted deliberately and intentionally killing Katie in a hotel room.
He said his client had been seeking psychiatric help after being convicted of making threats to kill in Bristol.
Miss Locke's family were in court for the hearing. In a statement released by police at the time of her death, they said: "As a family we are distraught, in shock and totally devastated. There was not a bad bone in Katie's body.
"Katie worked hard and loved her job as a teacher. In what little spare time she had she enjoyed sports.
"We now feel like our future has been stolen from us."
Lawyers representing the first husband and father of alleged "honour killing" victim Samia Shahid say they will seek to have the case thrown out.
[NEXT_CONCEPT]
A 26-year-old lawyer has pleaded guilty to murdering a young teacher whose body was found at a hotel on Christmas Eve.