"Two people who infiltrated the Golan from Syria were expelled through Quneitra," a military spokeswoman said., referring to a crossing post situated on the United Nations-supervised armistice line between Syria and Israel.
Israeli army radio said the protesters were a man and a woman but no further details were available.
Thousands of protesters gathered on the armistice line on Sunday and dozens crossed over into the occupied Golan Heights.
Four people were killed when Israeli troops opened fire on the demonstrators. Another 10 protesters were killed on the Lebanese border.
Israeli police were still searching for remaining infiltrators on Tuesday morning, manning road blocks and continuing house-to-house searches in Majdal Shams, the largest pro-Syrian town in the Golan.
Two other Palestinians detained on Monday remained in custody, with one of them, Hassan Hijazi, expected to appear in court on Tuesday afternoon to face accusations of illegally entering Israel, army radio reported.
Hijazi, a 28-year-old employee of the Syrian education ministry, managed to travel from the Golan all the way to Jaffa, on Israel's Mediterranean coast.
He told reporters his family was originally from Jaffa and lost their homes along with tens of thousands of other Palestinians who fled or were forced out in fighting that accompanied the creation of Israel in 1948.
He turned himself in to police after talking to reporters on Monday afternoon and expressing pride at reaching Jaffa, now a mixed Arab-Jewish district of Tel Aviv.
"This isn't Israel, this is my country," he said. "I don't want to go back to Syria. I want to stay here where my father and my great-grandfather were born and bring my family here," he said.
There were no details on what action was being taken with the fourth infiltrator in Israeli custody.