A lawyer argued that a pardon would be illegal while the case was pending in the courts.
"Since the matter is in the high court, the government cannot now make any move to pardon Bibi," lawyer Allah Bakhsh Leghari told Agence France-Presse.
Asia Bibi was sentenced early this month to death by hanging for allegedly speaking against the Prophet Muhammad. The Christian mother of five is the first woman to receive a death sentence for blasphemy in Pakistan.
Bibi's attorney filed an appeal and signed a petition pleading for a presidential pardon.
Religious leaders, including Pope Benedict XVI, and human rights groups have called for her release but conservative Muslims have threatened anarchy if President Asif Ali Zadari pardons the woman.
Federal Minorities Minister Shahbaz Bhatti said he expects Bibi to be freed. He was tasked with investigating the accusations against Bibi and said preliminary findings showed she was innocent.
Bibi was arrested in 2009 following a petty argument she had with fellow field workers. She was picking fruit in a field with fellow Muslim workers and went to get water for the group. Upon returning, the Muslim women refused to drink the water because the container had been touched by a Christian.
Bibi was offended and argued with the women, but afterwards thought nothing of the incident. However, a few days later dozens of Muslims dragged her away and she was accused of blasphemy against the Muslim Prophet Muhammad, which she denies.
Human rights group Christian Freedom International warns that Bibi's case could set a precedent in the Muslim-majority nation where Christians are already harassed and persecuted regularly.
"If Asia is put to death, it could mean a rise in prosecutions of Christians – not just in Pakistan, but also in other nations where Islamic law is enforced," the group warned.
In the past, Pakistan's courts have issued death sentences for blasphemy, but no executions have been carried out. All the death sentences were thrown out upon appeal.