The Israeli army said on Monday that no one was hurt and that the troops did not shoot back in an effort to avoid escalation.
"There was shooting from Syria towards an Israeli force south of [the Syrian city of] Quneitra," an army spokeswoman said about the incident on the occupied Golan Heights.
"The Israel Defence Forces did not respond in order to maintain restraint. A protest was lodged with the United Nations [peacekeeping] force," she said.
Syria denied the accusation.
"This is not true ... the matter has to do with some kids playing with fireworks to celebrate the anniversary of the liberation of Quneitra from Israeli occupation in 1974," an official Syrian source told reporters.
The Syrian source added an investigation was made by a patrol from the United Nations Disengagement Observer Force on the strategic plateau that supervises an Israeli-Syrian ceasefire reached after the 1973 Middle East war.
Israeli media reports said the soldiers were repairing a border fence when they came under fire from a Syrian army position. Violence is rare on the Golan Heights, captured by Israel in the 1967 Middle East war.