CBI special judge SK Yadav passed the order on applications moved by former Deputy Prime Minister Advani (89), ex-union minister Joshi (83) and Ms Bharti (58) seeking exemption from personal appearance on different grounds.
Allowing the plea, the court, however, said the three would have to appear before it as and when directed.
Counsel for the BJP leaders had cited old age of Mr Advani and Mr Joshi, and extensive travel by Ms Bharti as reasons for their inability to appear before the court daily during the trial.
They were granted a similar relief during the trial proceedings in the case in Raebareli.
The Supreme Court had on April 19 transferred the Raebareli case to Lucknow for a joint trial in the two cases relating to the demolition.
There are 34 accused in the case and the CBI court is conducting the day-to-day trial on the direction of the Supreme Court.
During today's proceedings, the CBI got a prosecution witness, Ramakant Dubey, discharged on the ground that it did not require him for recording of evidence.
The special court had on May 30 framed the serious criminal conspiracy charge against BJP leaders Mr Advani, Mr Joshi, Ms Bharti and nine others and allowed the prosecution to begin the trial.
Their application for discharge from the offence was rejected by judge SK Yadav.
The court had also granted them bail on a personal bond of Rs 50,000 each.
It had ordered the restoration of the conspiracy charge against the three leaders.
This charge against them had been dropped by a trial court in 2001 and the verdict had been upheld by the Allahabad High Court in 2010.
Besides the three senior BJP leaders, party MP Vinay Katiyar, one-time Hindutva firebrand Sadhvi Rithambara, VHP's Vishnu Hari Dalmiya, Mahant Nritya Gopal Das, Mahant Dharam Das Maharaj, Ram Vilas Vedanti, Champat Rai Bansal, Baikunth Lal Sharma and Shiv Sena leader Satish Pradhan are the other accused against whom charges have been framed by the special court.
The 16th-century mosque in Ayodhya was pulled down on December 6, 1992.
The Supreme Court had called the destruction of the mosque a "crime" which shook the "secular fabric of the Constitution" while allowing the CBI's plea seeking restoration of the criminal conspiracy charge against Mr Advani and others.
The accused are also facing charges of having made assertions "prejudicial to national integration and injuring or defiling a place of worship".
The other charges against them include indulging in "deliberate and malicious" acts intended to outrage religious feelings, uttering statements leading to public mischief, rioting and unlawful assembly.
The maximum punishment which could be awarded to Mr Advani and others upon conviction in the matter, could be up to five years imprisonment or fine or both, according to a lawyer.