The case was registered on the complaint of advocate Farhat Manzoor, who said that the video hurt the religious sentiments of the public.
The FIR has also appealed for stern action against the mosque administration and production house responsible for the video.
Qamar and Saeed came under harsh criticism for purportedly shooting a music video in the historic mosque. However, both have since apologised to the public in video messages.
“We realise what has happened over the past few days has hurt your sentiments deeply,” Saeed wrote as a caption. “We as Muslims, as decent human beings and as artists will never, ever trivialise or condone disrespect to Islam or any other religion, race, caste, colour or creed. If we have unknowingly hurt anyone’s sentiments we apologise to you all with all our heart," he added.