A notice to airmen (NOTAM) issued by the Aviation Authority on Wednesday notified the changes. It said that all Karachi-bound flights will have to abide by the modifications from August 28 to August 31.
The minister had on Tuesday tweeted: "A complete ban on the use of Pakistan's land routes for Indian trade to Afghanistan was suggested in the Cabinet meeting."
During the Cabinet meeting, Khan had objected to the use of Pakistan's airspace by Indian Prime Minister Narendra Modi, media reports said.
Modi used Pakistan's airspace to travel to France on August 22. He was given permission to use Pakistani airspace because there was no ban in place, the Cabinet was told on Tuesday.
This isn't the first time Pakistan has closed its airspace this year. A complete closure was put in place after the Balakot strike by the Indian Air Force on February 26.
The airspace was completely opened on July 16, five months after tensions escalated in February following the Pulwama terror strike in which 40 Indian security personnel were killed in a Jaish-e-Mohammed suicide attack.
The latest tensions between the two countries started on August 5, after India ended the special status of Jammu and Kashmir.
In his address to the nation on August 26, Prime Minister Khan had termed the Bharatiya Janata Party (BJP)-led government's move to revoke Kashmir's special status as a "historical blunder".
He said Pakistan had received information that India was planning to stage a "false flag operation" in Kashmir to justify a possible attack on Pakistan.
"Our Army has prepared itself after we received the information," Khan said.
He urged the world to intervene to ease tensions between the two countries, saying that India and Pakistan both have nuclear weapons.
( With inputs from IANS )