Mr Perez, 70, who was elected for a second term in 1989, has promised to respect the court's ruling and should now step down pending trial by the Supreme Court. A caretaker president will take over until Congress elects a replacement.
As a tense country awaited the court's decision, thousands of police patrolled the streets of the capital, Caracas. Mr Perez survived two army coup attempts last year, and there are fears violence could again break out.
The impeachment process began when the Public Prosecutor, Ramon Escovar Salom, took up an accusation by a veteran left-wing politician, Jose Vicente Rangel, that Mr Perez had misappropriated dollars 17.2m ( pounds 11m) in funds assigned to the Interior Ministry in 1979. The President denied the charge but refused to give a detailed explanation of what happened to the money.
The country has become polarised between supporters and detractors of the President. Recent opinion polls have given Mr Perez a popularity rating of less than 10 per cent.
Many observers fear that the armed forces, which are also badly split, will decide to take over if disorder threatens to get out of hand. More than 200 people died in the second of last year's unsuccessful coups, in November, when junior and senior army officers joined left-wing civilian groups in trying to overthrow the government. The high command remained loyal on that occasion.
Mr Perez was President during the oil boom years of the mid-1970s, when Venezuela enjoyed unprecedented prosperity. It also became one of the region's most stable democracies after the last military regime was ousted in 1958. But Mr Perez' second term has been marked by dwindling revenues and harsh austerity policies, bitterly resented by the millions who felt excluded from the earlier bonanza. It is officially estimated that around 35 per cent of Venezuela's 20 million people live below the poverty line.
Matters have been made worse by the rampant corruption that characterises Venezuelan politics, with two main parties, the ruling Democratic Action and the Christian Democrat party, Copei, dividing up the spoils.