The dispute between the Supreme Court and the president is likely to become a distraction for a government struggling to fight Islamist militants and to get a sluggish economy on track.
A confrontation between the Supreme Court and former president Pervez Musharraf blew up in 2007 and undermined the authority of Musharraf, who stepped down months after his allies were defeated in a February 2008 general election.
The latest confrontation has been brewing for some weeks over appointments to the Supreme Court and provincial high courts.
Zardari on Saturday issued an order appointing two judges, Khawaja Sharif and Saqib Nisar, as judges of the Supreme Court and chief justice of the high court in the city of Lahore respectively.
But hours later the Supreme Court blocked the appointments.
A Supreme Court panel said the president’s appointment order had been suspended because Zardari had apparently violated the constitution by not consulting Chief Justice Iftikhar Chaudhry.
The Dawn newspaper said in an editorial the country was facing a “highly arcane and technical dispute over constitutional prerogatives between the executive and the head of the superior judiciary”.
“(The dispute) nevertheless carries the potential for having seriously destabilising effects on the polity,” the newspaper said on Sunday.
“Historically, clashes between these two institutions have led to disastrous consequences for democracy and constitutional continuity,” it said.
The row occurred two months after the Supreme Court threw out an amnesty that had protected Zardari, several top aides and thousands of political activists and civil servants, mostly from corruption charges.
The end of the amnesty sparked a political storm and raised questions about Zardari’s future, even though he is protected from any prosecution by presidential immunity.