General Qamar Javed Bajwa has served three years in his role, arguably the highest authority in the country, and in August Prime Minister Imran Khan asked him to extend his tenure and serve another three.

The request is not unusual. The Pakistani military has long played an outsized role in national life, ruling the country for roughly half its 72-year history, while many army chiefs have gone well beyond their mandated term.

This time, however, the Supreme Court has raised questions about the legality of the decision, in an unexpected move that has shocked the South Asian nation long accustomed to seeing the military get its way.

Oh Thursday, hours ahead of the midnight deadline for Bajwa's term to expire, the court said it was granting him a conditional extension of six months, giving parliament time to clarify the consitutional guidelines under which an army chief's tenure could be prolonged.

"Considering that the (army chief) is responsible for the command, discipline, training, administration, organisation and preparedness for war of the army ... we, while exercising restraint, find it appropriate to leave the matter to the parliament," Chief Justice Asif Saeed Khosa told the court.

Khan celebrated the court's decision.

"Today must be a great disappointment to those who expected the country to be destabilised by a clash of institutions," the prime minister tweeted moments after the ruling.

But the episode has damaged Khan's administration, which is seen as close to Bajwa.

"This is a landmark case: unprecedented questions are being raised, threatening to upend the accepted status quo, and holding a mirror to society's psyche," Pakistan's leading English daily Dawn wrote in an editorial earlier Thursday.

Bajwa was appointed to lead the military in 2016, taking over from the massively popular General Raheel Sharif, who won the hearts of millions with his blistering fight against Islamist militants.

Since taking power, Bajwa and the military have been criticised for continuing a crackdown on civil society while also being accused of helping engineer Khan's victory in the 2018 elections.

The government itself is facing growing anger as it struggles to prop up Pakistan's economy after decades of corruption and mismanagement.

The debate over the army chief's tenure -- accompanied by swelling calls from the public on social media for the general to step aside -- has raised fresh questions over Khan's ability to stay in office in a country where not a single prime minister has ever completed their term.

Bajwa is the latest in a long line of Pakistani military generals who have seen their mandates extended.

The ruling comes as tensions have skyrocketed with New Delhi after Prime Minister Narendra Modi stripped the disputed Kashmir region of its autonomy over the summer, which Khan's government cited as its primary reason for the extension.

Both India and Pakistan have controlled portions of the former princely state of Kashmir since independence in 1947.

The dispute over the Muslim-majority region has been the spark for two major wars and countless clashes between them.