Bharti, along with BJP veterans L K Advani and Murli Manohar Joshi among others, was charged by a special CBI court in Lucknow and also granted bail in the case.
The court framed charges under Section 120-B (criminal conspiracy) of Indian Penal Code against the BJP leaders.
Naidu told reporters the accused BJP leaders are "innocent" and will come out of the case "unscathed".
Arrival of the BJP veterans for the court appearance prompted the party's Hindutva faces to raise the pitch for the construction of Ram Temple.
Chief Minister Yogi Adityanath too met Advani.
BJP MP Sakshi Maharaj said "no power on earth" could stop the construction of the Ram temple in Ayodhya.
Bharti, the Union minister of water resources, said before appearing in the court that the mosque was pulled down not as part of a "criminal conspiracy" but an "open movement".
"I was present in Ayodhya on December 6, 1992, which is no secret. Crores of BJP workers, lakhs of officials and thousands of political leaders participated.
The Congress asked Prime Minister Narendra Modi to uphold the law and the Constitution by getting Bharti to quit as minister.
"One of the accused, Uma Bharti is a Union Cabinet minister. Having been charge-sheeted, she must resign. Prime Minister must come forward and uphold the rule of law and the Constitution," AICC incharge of communications Randeep Surjewala said.
"Time for law of the land to deliver justice expeditiously," he said as the opposition party voiced hope that the trial will now begin.
Another BJP leader and one of the accused, Vinay Katiyar, insisted that there was no conspiracy as the mosque was razed by a big crowd in the open.
"It is not appropriate to charge a few persons with criminal conspiracy," the one-time firebrand Hindutva leader and former UP BJP chief said.
Katiyar targeted Samajwadi Party leader Mulayam Singh Yadav saying that a case should have been lodged against the former chief minister over the firing by police on 'kar sewaks' in Ayodhya in 1990.
He also claimed that the case had "reached" the judgement stage before the apex court gave its new ruling.
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