President Nicolas Maduro said the diplomats have 48 hours to leave the country, saying “Yankees, go home!”
Mr Maduro says he has evidence that the trio took part in a power-grid sabotage in September and had bribed Venezuelan companies to cut down production.
The United States and Venezuela have been without ambassadors in each other’s capitals since 2010.
The diplomats expelled have been named as Kelly Keiderling – the charge d’affaires and the most senior US diplomat in Caracas – David Moo and Elizabeth Hoffman.
“We completely reject the Venezuelan government’s allegations of US government involvement in any type of conspiracy to destabilize the Venezuela government,” the embassy said in a statement.
It said it had not yet been officially notified of the Venezuelan government decision to expel the three diplomats.
Mr Maduro made the announcement during an official ceremony at the city of Santa Ana.
“Out of Venezuela! Yankees go home! Enough of abuse against the dignity of a peace-loving nation,” he said.
Venezuela is facing a shortage of several goods, including toilet paper, sugar and flour.
The opposition blames Mr Maduro’s left-wing policies and rhetoric for the crisis.
‘New York plot’
Relations between the two countries have been bad for over a decade.
For years, the late President Hugo Chavez denounced “American imperialism” in Latin America.
In December 2010, Chavez denied a visa to the man appointed to be US ambassador to Caracas, Larry Palmer, over remarks he had made about involvement between the Venezuelan government and Colombian Farc rebels.
“Anyone who comes here as an ambassador has to show respect. This is a country that must be respected,” Chavez said at the time.
The US retaliated and expelled the Venezuelan ambassador to Washington.
Mr Maduro took office as interim president when Chavez was terminally ill with cancer. He was elected president in April, by a narrow margin, defeating opposition leader Henrique Capriles.
Mr Maduro’s new Foreign Minister, Elias Jaua, met the US Secretary of State, John Kerry, during a regional summit in Guatemala in June.
They both said they were determined to improve relations, but the good will did not last long.
Last week, Mr Maduro cancelled his scheduled speech at the United Nations Assembly General, saying that his life would be in danger in New York.
Mr Maduro accused two former US officials of being behind the “provocations”.
“The US government knows exactly that these people were behind a dangerous activity being plotted in New York,” he said.