They were injured after "drone, mortar and light weapon attacks" from "PKK/YPG terrorists" while conducting reconnaissance and surveillance in the Ras al-Ain region, the ministry said on Twitter.
It said they retaliated in self defence, but gave no further details.
Under the October 17 United States-Turkey agreement, Ankara and its Syrian proxies have control over the 120-kilometre (75-mile) stretch of territory between Ras al-Ain and Tal Abyad after Kurdish fighters agreed to withdraw from the area.
The deal came after Turkey launched a cross-border offensive against the US-backed Syrian Kurdish People's Protection Units (YPG) militia on October 9, which led to immediate international condemnation.
The US said Tuesday that the YPG pullout had been completed after Turkey suspended its operation for five days.
Washington then lifted sanctions on Turkey after Ankara completely ended the offensive.
For Ankara, the YPG is a "terrorist" offshoot of the outlawed Kurdistan Workers' Party (PKK), responsible for an insurgency against the Turkish state since 1984.
The PKK is proscribed as a terror group by Ankara, the US and the European Union.
Also on Thursday, Mustafa Bali, a spokesman for the Syrian Democratic Forces (SDF) -- made up largely of Kurdish YPG forces -- accused the Turkish army and its Syrian proxies of bombing several villages in north-eastern Syria.
The "SDF will exercise its right to legitimate self defense and we are not responsible for the violation of the agreement," Bali said on Twitter.
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