Islamabad turned down the request based on the "alarming human rights situation in Indian-occupied Kashmir (IoK)", announced Pakistan's Foreign Minister Shah Mehmood Qureshi.
Qureshi said Prime Minister Imran Khan had approved of the decision to reject the request and added that "the Indian aggression in IoK" was responsible for Pakistan's move.
The Minister added that Pakistan had shown "restraint" in reacting to India's move in Kashmir but that New Delhi was "refusing to budge from its stubbornness and denying basic facilities to the residents of occupied Kashmir".
"In view of this, we have decided to not allow the Indian President to use our airspace," he told PTV.
Islamabad's decision comes amid tensions between the two neighbours over New Delhi's revocation of the special status to Jammu and Kashmir on August 5.
Qureshi also said New Delhi's "barbarism" in Kashmir was a serious issue which he would take up with the UN Human Rights Council.
He added that "34 days have elapsed since Indian authorities imposed a crippling curfew in occupied Kashmir" after revoking the region's special autonomy.
In August, it was reported that Khan was considering shutting down Pakistani airspace for India. A complete ban on Indian trade to Afghanistan through Pakistani land routes was also under discussion, reports say.
Pakistan's Minister for Aviation Ghulam Sarwar Khan had told a press conference earlier this week that their government had so far not taken any decision to close the eastern airspace to commercial flights from India; however "we have reserved the right to do so and it would be utilized at an appropriate time".
( With inputs from IANS )