The court gave him until 25 July to ask the Swiss authorities to reopen previous cases, or face legal action.
In June the court disqualified Yousuf Raza Gilani as PM after convicting him of contempt for failing to pursue corruption cases against Mr Zardari.
He had argued that the president had immunity from prosecution.
The court issued its order late on Thursday. The moves are being seen as part of a long and bitter feud between the judiciary and the civilian government, which also has a troubled relationship with the powerful military.
The corruption charges against President Zardari date back to the 1990s, when his late wife Benazir Bhutto was prime minister. They were accused of using Swiss bank accounts to launder bribe money.
President Zardari has always insisted the charges against him are politically motivated.
Observers say Pakistan can ill-afford its constitutional in-fighting. The country’s economy is in crisis, as are relations with the US, and militants are waging a violent insurgency in tribal areas near the Afghan border.
General elections are due by early next year, with the Pakistan People’s Party-led government aiming to make history by becoming Pakistan’s first civilian government to see out a full five-year term.