It is the first time that Israel has confirmed a ground operation in Syria, which is close to Iran.
The Israeli military did not specify where in Syria the ground operation took place, nor exactly when the capture was made – but only states that the operation was carried out "in recent months".
The London-based Syrian Human Rights Observatory (SOHR) had previously reported that a Syrian man was captured by Israeli forces in July.
Israel has named the captured man and claims that he gathered intelligence on the Israeli military in the border areas, information that would lead to "terror activities" on the Israeli-occupied Golan Heights near the border with Syria.
The terrorist activities are said to have been initiated by Iran, claims Israel, which also states that the captured man was monitored for months and has been taken to Israel for questioning.
Syria has not commented on the reports.