Earlier in the day, Jordan gave Syrian Ambassador Bahjat Suleiman, a former general and intelligence chief, 24 hours to leave the country.
The envoy was accused of having made repeated public criticisms of the kingdom. He criticized Jordan's Western backed policy against Syria.
Jordan said on Monday it was expelling Syria's ambassador for accusing the kingdom of backing Syrian militants, prompting Damascus to retaliate by barring Jordan's top diplomat.
Jordanian officials said the charge d'affaires was not currently in Syria.
Suleiman has accused Jordan in his posts of hosting radicals sent to fight President Bashar al-Assad's army and of providing a haven for hundreds of Syrian army defectors training them with Saudi help to go back and join militant groups.
Suleiman allowed his followers on Facebook to leave comments strongly critical of Saudi Arabia and other Persian Gulf Arab states which back the Syrian militant groups.
Suleiman's expulsion was tied to the embassy's announcement it will stage voting for one million Syrians living in Jordan in a presidential election on June 3.
Earlier this month, Foreign Minister Nasser Joudeh claimed that allowing the Syrian embassy to organize voting could bring security problems in the country.
Syrian authorities say holding the elections would be a major milestone towards ending the conflict.
NJF/NJF