Turkish police used tear gas and water cannons to disperse the students who tried to march to the Foreign Ministry.
The demonstrators censured Turkish Prime Minister Recep Tayyip Erdogan’s policies of funding and supporting the foreign-backed militants operating inside the Arab country.
According to human rights advocacy group, Bianet, about 30 students were arrested and at least two students were injured in the clashes.
Wednesday's protest comes days after two powerful car bombings in a town near Turkey's border with Syria killed 51 people.
Ankara rushed to accuse Damascus of masterminding without providing any evidence. Syria rejected the accusations and said it is willing to carry out a joint investigation with Turkey into deadly attacks.
Turkey has been one of Syrian President Bashar al-Assad's harshest critics and has supported the foreign-backed militants fighting to topple his government.
Turkish opposition parties have censured the Turkish government for its intervention in Syria’s internal affairs.