The US State Department also urged Americans to reconsider any plans to travel to Jordan.
The move follows the still unsolved killing of US diplomat Laurence Foley in the capital, Amman, last month.
Jordan said it "regretted" the US decision but added that relations between the two countries were "excellent".
The State Deprtment has issued a spate of warnings to US citizens abroad, including two "worldwide cautions" this month.
Prudent measure
State Department deputy spokesman Phillip Reeker said: "We think it's a prudent measure designed to allow some embassy employees and dependents to depart post, should they decide to do so".
Under the so-called "authorised departure" scheme, non-essential diplomats and the families of embassy employees are allowed to return home at Washington's expense.
The US Secretary of State, Colin Powell, explained the move to Jordan's King Abdullah, who was "understanding," Mr Reeker said.
But Jordan's Minister of State for Political Affairs, Mohammad Adwan, insisted that "Jordan is still one of the safest and most secure countries in the world that protects all its foreign guests".
Shot dead
Mr Foley, a US Agency for International Development (USAID) official, was gunned down outside his home in west Amman on 28 Ocotber.
Nobody has been arrested in connection with the killing and the motive remains unknown.
Earlier this week, Mr Reeker praised the Jordanian authorities for their investigations.
"Jordanian security forces have been making extraordinary efforts and we've been working closely with them to investigate that killing and also to provide protection for Americans in Jordan," he said.
"We're very confident of those efforts, that they will ultimately be successful and bring to justice the murderer or murderers of Mr Foley."
Mr Reeker said there had been no specific threats against Americans in Jordan since Mr Foley's death, but the State Department said there was a general threat against US citizens in the Middle East and North Africa as a whole.