A traders' union organised a protest in the central city of Multan against the judgement to split the disputed site between Hindus and Muslims.
The members of the union shouted slogans against the court's ruling. The Sunni Tehrik organised a protest at Hyder Chowk in the southern city of Hyderabad.
Dozens of protesters shouted slogans and burnt tyres. Members of the Sunni Tehrik rejected the court's verdict, saying it went against the wishes of Muslims.
They said they would organise more protests if the Pakistan government accepts the court's ruling. They also called on the government to sever diplomatic and economic ties with India.
At both Multan and Hyderabad, the protestors burnt effigies and posters of Indian leaders.
In Islamabad, Religious Affairs Minister Kazmi said the Indian court had issued a "political verdict" on the Babri mosque issue that was "totally in favour of the Hindu community".
Muslims in India have been deprived of their rights due to the one-sided decision on the Mosque, Kazmi told state-run PTV.
"The court cited Babri mosque as the birthplace of (Lord) Ram and recommended a little piece of land for Muslims like a donation," he said.
The decision to distribute the land among Muslims and Hindus is complicated and will create problems for the faithful in offering prayers, he claimed. He asked Indian Muslims to file an appeal in the Supreme Court and to make more efforts to protect their rights.
"In Pakistan, we have always raised our voice against any injustice with the minority communities, while in India, the state is not showing solidarity with the Muslims," he alleged.
Kazmi asked people from all walks of life to raise their voice against the "unjust decision".
Some religious leaders condemned the court's verdict, saying it disclosed the real face of India.
"We condemn this verdict. We reject it as well. This will create resentment on an international level," said Sahibzada Fazle Karim, a senior member of the Jamiat Ulema-e-Pakistan.
The Organisation of the Islamic Conference should take serious steps on the issue, he contended. Noted cleric Allama Abbas Kumaili described the decision as unjustified.
"We condemn the court's verdict," he said. He claimed the court was under the "influence of the majority Hindus. It is a diplomatic decision," said Ruet-e-Hilal Committee chief Mufti Muneeb-ur-Rehman. He said Indian Muslims should keep the peace.
"I appeal to Indian Muslims not to take to violence. The way of protests should be peaceful," he added.