Police moved in to disperse them, sparking clashes and rock-throwing.
Micky Rosenfeld, a police spokesman., said about 200 people had gathered outside the village and a number of the protesters had broken through the police barrier.
"Stones were thrown and 13 people were arrested," he said.
No one was injured.
The attack on the seminary earlier this month was the deadliest Palestinian attack on Israelis in two years and the first major attack in Jerusalem for four years.
The assault on the yeshiva, closely allied to Israel's Jewish religious nationalist movement, brought calls for revenge from extremist rabbis and demands for punitive measures against Abu Dhaim's family from several Knesset members.