According to Geo News Islamabad turned down the request based on the alleged "alarming human rights situation" in Jammu and Kashmir.
Qureshi, according to media reports, 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.
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.
Qureshi 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" before revoking the region's special autonomy.
Though Pakistan has been threatening to completely close its airspace for India since the latter announced its decision to abrogate Article 370, no official notification had come in this regard. Following India's historic decision, Islamabad has downgraded its diplomatic relations with India and partially closed its airspace.
However, Prime Minister Narendra Modi last month used the Pakistani airspace to travel to France for a bilateral meet.
Islamabad has shut its airspace earlier following the Indian Air Force (IAF) action on February 26. IAF planes had destroyed terror camps in Pakistan's Balakot area, following the February 14 Pulwama terror attack which killed over 40 CRPF personnel in Jammu and Kashmir. On July 16, Pakistan had fully opened its airspace for all flights.
(With inputs from agencies)