"We had filed an application in the court seeking bail on the grounds that she was not involved in the case and there is no case made out against her," her lawyer Rameshwar Gite said.
The court rejected her bail application, Gite said, adding that they are now likely to move the Bombay High court.
Earlier, the court had also rejected her bail application filed on medical grounds, in which she had said that she needs to be operated for her lumber spondylitis.
Twelve persons, including Sadhvi Pragya and Lt Col Prasad Purohit, were arrested for carrying out blast in Malegaon on September 29, 2008, in which six persons were killed and 100 others injured.
The accused have been booked under the stringent Maharashtra Control of Organised Crime Act (MCOCA), Unlawful Activities Prevention Act (UAPA), besides the Indian Penal Code (IPC).
The trial is yet to commence as some of the accused have challenged the invocation of MCOCA in the case before the Supreme Court, which is pending.