The abductions were made on Tuesday with Israeli officials claiming that the captives were involved in Monday's clashes when Palestinians gathered inside a mosque at the site and threw firebombs and rocks at Israeli forces outside.
The development comes amid a flare-up of tensions in and around the compound in recent weeks.
On Monday, skirmishes broke out in the holy site after the deployment of Israeli soldiers to the area for the Jewish Sukkot holiday.
Also on Sunday, clashes erupted across the compound after Israeli police stormed the holy site and fired rubber-coated steel bullets and stun grenades at Palestinian protesters.
Meanwhile, more clashes were reported on Tuesday between Israeli forces and Palestinian demonstrators protesting cross the occupied West Bank in support of the al-Aqsa Mosque, Press TV reported.
According to Palestinian media reports, twelve protesters sustained injuries as Israeli forces attacked a rally near Ramallah.
Israeli forces used tear gas and water cannon, as well as live fire, and rubber-coated steel bullets to disperse the protesters who were angry at Israel's restrictions on prayers in the holy site.
Dozens of youths also suffered tear gas inhalation in the city of Bethlehem as Israeli forces attacked a protest rally near Aida refugee camp.
Furthermore, in the nearby village of Tuqu, a number of schoolchildren inhaled tear gas after Israelis opened fire at a pro-Aqsa demonstration.
Similar skirmishes were also reported in the city of Tulkarem where Israeli forces attacked demonstrators marching to voice solidarity with the al-Aqsa Mosque.
Israeli soldiers have attacked and injured dozens of Palestinians in rallies held against Tel Aviv’s military assaults on the al-Aqsa Mosque, which started on September 13.
The recent wave of violence has seen Israeli settlers and soldiers attacking Palestinian worshipers following the deployment of Israeli troops to the area for the Jewish Rosh Hashanah New Year holiday.
Last month, Israel imposed harsh restrictions on entries into the al-Aqsa Mosque, especially limiting the entry of Palestinians into the compound.
The al-Aqsa Mosque is Islam’s third holiest site after Masjid al-Haram in Mecca and Masjid al-Nabawi in Medina, Saudi Arabia. Its compound is also highly respected by Jews and Christians.