In a statement read out on state television, Syria said the Turkish government had informed the Syrian consulate in Istanbul about the operation to relocate the tomb of a figure revered in Turkey, but had not awaited Syria's agreement.
Turkey mounted the operation to extract about 40 soldiers who had been guarding the Tomb of Suleyman Shah, grandfather of the founder of the Ottoman Empire which is on a site considered sovereign territory by Ankara.
Syria accuses Turkey of supporting insurgent groups that have seized control of wide areas of northern and eastern Syria, including the ISIS militant group.
The Syrian government statement said the fact that ISIS had not attacked the tomb "confirmed the depth of the ties between the Turkish government and this terrorist group".
In line with its hardline vision of Islam, ISIS has blown up many tombs in areas under its control.
Syria said the operation was a violation of an agreement signed in 1921.