Israeli soldiers also used tear gas and pepper sprays against the Palestinians during Tuesday attack.
The prayers were “harshly beaten and dragged on the ground” by the Zionist forces, according to the witnesses.
Eight people were injured by electric shockers used by the Israel forces.
One of the Palestinians, who has been severely beaten with batons, is in critical condition and has been taken to hospital.
Witnesses identified the abductees as Jameel al-Abbasi and Saeed Abu Jamal.
Israeli regime authorities gave no explanations on reasons of the Tuesday attack.
The attack comes as extremist Jewish groups called on Israeli settlers to gather around al-Aqsa Mosque on Tuesday to invade the holy site.
Israeli forces frequently attack prayers at al-Aqsa which is the third holiest place for Muslims in the world. Women are banned by Israeli forces to enter the mosque and no men under the age of 50 years are allowed to pray in the holy site.