The three are accused of inciting Hindu zealots to pull down the 16th century Babri mosque in 1992, igniting one of India's most explosive religious disputes in which thousands died.
The demolition of the mosque marked the culmination of a virulent campaign led by the now ruling Bharatiya Janata Party (BJP).
India's top court said government minister Uma Bharti, former deputy prime minister L K Advani and M M Joshi - all senior BJP members - should face criminal conspiracy charges, according to the Press Trust of India news agency.
#SC allows CBI's appeal in #BabriMosque demolition case and restores criminal conspiracy charge against #LKAdvani & other BJP leaders.
— Press Trust of India (@PTI_News) April 19, 2017
The ruling came after a lower court dropped the charges brought against them by India's Central Bureau of Investigation (CBI), kicking off a series of appeals and counter-appeals.
"We have allowed the CBI appeal against the Allahabad High Court judgement with certain directions," the news agency quoted the Supreme Court judges as saying.
India's apex court urges 'negotiated settlement' for Babri mosque dispute
Many Hindus believe the Babri mosque was only built after the destruction of a temple that marks the birthplace of their god Ram.
Some in the BJP, which recently won elections in India's largest state Uttar Pradesh, want to build a temple to Ram on the ruins of the razed mosque - an idea that horrifies the state's significant Muslim minority.
Indian media said the charges would scupper the chances of Advani, now 89, of becoming India's next president when the role becomes vacant later this year.
He was present on the day of the demolition, which sparked nationwide riots and thousands of deaths and came to define his political career.
However, in a later interview with the BBC, he said the incident had hurt him "tremendously" and should never have happened.
Poster for temple in place of Babri Masjid carries Muslim cleric’s photo
There was no immediate reaction from the BJP, but the opposition Congress said the ruling party had "tried every trick in the book" to ensure that Advani, Bharti and Joshi did not face charges.
"What they (Supreme Court) have said today means there's clinching evidence that needs to be now argued out in the court," said party spokesperson Sanjay Jha.
The court also ruled that a fourth senior BJP politician, Kalyan Singh, who was leader of Uttar Pradesh at the time of the incident, should face criminal conspiracy charges.
His trial, however, will be delayed until his stint as governor of Rajasthan state is over because the position of governor gives him immunity from prosecution.
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