The court ordered Mr Gilani to appear before it on 13 February. If convicted he could face six months in jail and would be barred from office.
The government has refused to prosecute President Asif Ali Zardari, saying he has immunity as head of state.
Mr Zardari has rejected the corruption charges as politically motivated.
The BBC’s Orla Guerin in Islamabad says the Supreme Court decision is another twist in a case which could bring down the prime minister and his government.
The case comes at a time of intense political uncertainty, with the government at loggerheads with the country’s powerful military as well as the judiciary.
Pakistan has suffered three military coups since independence in 1947 but analysts believe the army has little appetite for a coup in this instance