Khalid Chishti was detained on September 1 on a charge of blasphemy for desecrating the Quran and planting evidence that was used against the girl Rimsha Masih.
He was arrested after his deputy Maulvi Zubair and two other men gave statements that Chishti had framed Masih.
Subsequently, two of the witnesses withdrew their statements and a court accepted Chishti's application for bail. He was freed after he paid a bond of Rs 200,000.
Masih spent three weeks in a jail after being arrested on August 16 for allegedly burning pages of a religious text.
After being freed on bail, she and her family were taken by authorities to an undisclosed location for security reasons.
The girl's case has also been transferred to a juvenile court after a medical board concluded that she was 14 and that her mental development did not correspond with her age.