Islamabad Civil Judge Saqib Jawad issued arrest warrant against Azizi on the request of investigation officer of the case.
The Aabpara Police Station had registered an FIR against Aziz two days ago under section 506 (2) (hurling threats) of the Pakistan Penal Code.
Members of civil society had been protesting outside the Lal Masjid agains Aziz for his unwillingness to condemn the brutal attack on the Army Public School in Peshawar that killed 150 people, mostly children.
Former military ruler Pervez Musharraf had launched a military action in the Lal Masjid in 2007 in which around 100 alleged militants, including the younger brother of Aziz, were killed.