A statement from the army Wednesday said the repatriation of the six "was completed at an undisclosed location for their own safety."
A seventh Syrian remains in the Ziv Hospital in northern Israel.
The return wasn't coordinated with the International Red Cross as that would have required them to enter Syria via the Quneitra border crossing and their entry coordinated with Assad's regime, Ynetnews.com said.
On Feb 16, seven Syrians, who approached the border with Israel in the northern Golan Heights, were found to have been injured. They were treated by Israeli military medics and taken to a hospital.
The seven were apparently wounded in clashes between rebel forces and Syrian army troops.
Throughout their stay in Israel, the hospital wards where they were treated were guarded and no details of their identities or photos were released.
The Israeli army described the entry of the group at the time as an "isolated" incident, one that doesn't reflect a change in Israel's policy against any breaches of the border fence "with the exception of special humanitarian cases."