Mohammad Hassan, 20, from Rina, and Ahmed Saida, 23, from Umm el Ghanam, were arrested in November, the Shin Bet said.
They had left Israel for Turkey in May, where they met up with an IS operative who was to help them steal across the border into Syria, where they were to join fighters, it said.
But after encountering Syrian refugees at the border town who told them of the horrors they suffered under IS, as well as their families' pleas, the two had a change of heart and returned to Israel, the statement said.
Identifying with the jihadist group's ideology, the two resolved to carry out an attack against Israeli Jews, and Saida attempted to purchase a rifle, Shin Bet said.
The two were charged today for links to foreign agents, an attempt to enter an enemy country and conspiring to commit a crime. Saida was also charged with weapons felonies.
Also today, the Jerusalem district court sentenced a Palestinian from east Jerusalem employed by Israel's health ministry to two years in prison for attempting to join IS forces in Syria in January.
Arab Israelis are those who remained in the Jewish state after its 1948 creation, as well as their descendants. They account for more than 17 percent of the country's population.
Police have said Israeli Arabs travelling to Syria to fight for IS represent "a serious threat to Israel."
According to the Shin Bet, around 35 Israeli Arabs have joined IS.
A number of them have died fighting with Islamist organisations, according to Israeli security and their families. Around 10 have returned to Israel and have been arrested or jailed.