Stern arrived with his family to pray, when stones and bags of water were thrown at him.
One person was taken in for questioning and other arrests are expected to follow.
The worshippers tried to prevent Stern from reaching the Western Wall and cried out, "traitor", "Go away you are not worthy of coming to the Western Wall," referring to his role in the recent disengagement from Gaza and the northern West Bank.
Police encircled Stern and his family and brought them to the Wall to pray under heavy security. One police officer was lightly injured from a stone thrown at him by one of the worshippers.
Police officers later escorted Stern and his family from the vicinity towards the Jewish quarter.
IDF Chief of Staff Dan Halutz expressed anger after hearing about the incident and slammed the violent act.
"There is no room for such behavior, definitely not one day after Yom Kippur where you expect everyone to behave with tolerance," he said.
Deputy Defense Minister Ze'ev Boim also slammed Friday's incident.
"This is unacceptable hooliganism that crosses all boundaries," he said. "Hooliganism is hooliganism, it doesn't matter what faith stands behind it. It's a pity the attackers behaved this way, at a place like the Western Wall on Shabbat eve."
- Hanan Greenberg contributed to the report