The Supreme Court stated that the trial will be held in the northern city of Lucknow and should be concluded in a period of two years.
On Wednesday, the apex court had said that no adjournment in the case would be given under normal circumstances and no judge would be transferred, who hearing the case, would be transferred, said ANI reports.
A former BJP leader, Kalyan Singh, presently the governor of Rajasthan, will be tried in the case after his term ends.
The Allahabad High Court ruling in 2010 addressed three major issues.
The three are accused of inciting Hindu zealots to pull down the 16 century Babri mosque in 1992, igniting one of India's most explosive religious disputes in which thousands died.
"It is a conspiracy, but we will follow the orders".
The Supreme Court today allowed the CBI's appeal and also ordered the clubbing of two trials that are now going on in the Babri demolition case. The court ordered that these persons would be tried for criminal conspiracy and the trial should be completed in two years.
"The government should immediately challenge the CBI's petition before the largest bench of the Supreme Court", he added.
In an initial reaction to the Supreme Court order restoring criminal conspiracy charge against top BJP leaders including L K Advani, M M Joshi and Uma Bharti, Congress chief spokesperson Randeep Surjewala said, "the Supreme Court has spoken". This would change with the judgment rendered by the Supreme Court today.
At first, there were two sets of cases relating to the Babri Masjid demolition on 6 December 1992.
The controversial Ayodhya land has been claimed by both the Hindu and Muslim communities with Hindus wanting to build a Ram Mandir on the Ram Janmbhoomi, while the Muslims want to rebuild the Babri Masjid.
It is pertinent to mention that the demolition of the mosque came after a movement led in part by Mr Advani for a temple to be built on the same spot where the masjid was constructed by the Mughals.
Senior lawyer and convener of the Babri Masjid Action Committee (BMAC), Jafarayeb Jilani said, "We are happy with the SC order and we had waited long for such directives". But then, he will be charged once he gives up the governor post.