The embassy as well as consulates in the Mediterranean cities of Alexandria and Suez were closed.
An official spokesman, quoted by SPA, said the measures were decided in response to demonstrations outside its missions in Egypt and threats following the announcement of the arrest of the Egyptian lawyer in Saudi Arabia.
The protests were "unjustified," the spokesman said, adding that Saudi and Egyptian employees of its diplomatic missions had been threatened.
"Hostile slogans were shouted out and the immunity of the diplomatic representations was violated, contrary to all international regulations," the spokesman said.
He said the violence had led to the suspension of diplomatic and consular services for Egyptian workers and Muslim pilgrims headed for Islam`s holiest sites, located in western Saudi Arabia.
On Tuesday, hundreds of Egyptians protested outside the embassy demanding the release of an Egyptian human rights activist held by Saudi authorities who claim he possessed banned drugs.
The protesters chanted slogans against the Saudi regime as they called for the "immediate" release of Ahmed Mohammed al-Gizawi, who was arrested on arrival at Jeddah airport on April 17.
The Arabic Network for Human Rights Information, an Egyptian organisation, said Gizawi was detained following a sentence of one year in prison and 20 lashes delivered against him in absentia for criticism of the Saudi government.
Gizawi, whose supporters said he travelled to the Gulf state on pilgrimage, was being targeted for his activism in favour of Egyptian detainees in Saudi prisons, it said.