Mr Johar's film stars Pakistani actors Fawad Khan, who has a sizeable fan following in India, and Imran Abbas.
"We have not put a ban ...we have suspended the release of the films where Pakistani artistes and technicians are involved," said Nitin Datar, the chief of the Cinema Owners and Exhibitors Association of India.
The association is largely linked to single screen cinemas, not multiplexes, and has members in Gujarat, Maharashtra, Karnataka and Goa.
A strong critic of the group's stance is one of its members, Censor Board chief Pahlaj Nihalani, who said there is no legal basis for the move. "Films already shot before changed relations between India and Pakistan should not be affected. Once cleared by censor board, the association does not have the right to ban or take decision not to screen a film," said Mr Nihalani.
He suggested a financial motive; Ajay Devgn's Shivaay also releases the same day as Ae Dil... and is seen as a better bet for single screens.
Other films that star Pakistani actors include Shah Rukh Khan-starrer Raees, Dear Zindagi and Mom but Mr Johar's film may be affected the most, even though losses are likely to be negligible since Ae Dil... is billed as a multiplex film with urban appeal.
Last month's terror attack in Kashmir's Uri, in which 19 soldiers were killed, and subsequent surgical strikes by the army in Pakistan-occupied Kashmir have ratcheted up tension between the neighbours and spurred calls for a wider disengagement from Pakistan - until ties are normal - in a variety of fields including films and sports.
A producers' body in Mumbai recently banned Pakistanis from working in Indian films. In retaliation, Pakistani theatre owners decided to stop screening Indian films.
Parties like Raj Thackeray's Maharashtra Navnirman Sena (MNS) have threatened to block Mr Johar's film if he does not drop Fawad Khan. The film industry has backed Mr Johar. "We are with the government but let the films that are already made release," said producer Mukesh Bhatt.