The surrender on Saturday ends a week-long hunt for the fighters in the mountain ranges on the border with Afghanistan.
The five men were expected to hand in a list of foreign fighters living with them in South Waziristan, a desolate region where al-Qaida leader Usama bin Ladin and his deputy Ayman al-Zawahiri have been hunted in the past.
Thousands of turbanned Pashtun tribesmen looked on as the five men from the Zali Kheil tribe turned themselves in before a "jirga", or tribal council, and pledged loyalty to Pakistan in return for clemency.
The deal also allows hundreds of alleged al-Qaida fighters to remain at liberty in exchange for pledges to live peacefully.
It also ends the Pakistani army's bloody hunt for Taliban guerrillas in the tribal region which has left more than 100 people dead.
Nek Muhammad, a former Taliban commander from the Yargulkhel sub-tribe, his uncles, Nur Islam and Muhammad Sharif, and Maulvi Muhammad Abbas and Maulvi Abd Al-Aziz had been at the top of a government wanted list since January for sheltering Afghan fighters.
Hundreds of tribesmen were gathering at Shakai to witness the proceedings.
Army corps commander Lieutenant General Safdar Husayn and Brigadier Mahmud Shah, security chief for the tribal territory, were scheduled to attend the ceremony.
Details of the deal mediated by tribal elders, including two members of parliament from the region, were not immediately available.
Several villages were razed
during government attack
Islamist lawmaker Mawlana Miraj al-Din said on Friday the government had agreed to give an amnesty to the rebels in return for a good behaviour pledge and allegiance to Pakistan.
He said foreign fighters living in the area would be allowed to stay, provided they registered with authorities and offered guarantees not to use Pakistan's soil to launch attacks against any other country.
The five men have been leading the fierce armed resistance to Pakistani army efforts in the tribal region to kill, capture or expel fighters linked to Usama bin Ladin's al-Qaida terror network.
The Pakistani army launched its largest operation in South Waziristan in March, capturing 167 tribesmen and foreign fighters.
The offensive left 46 troops and 64 fighters dead. At least 15 civilians were also killed.
About half of the estimated 600 fighters targeted in the operation escaped and are believed still to be hiding on the Pakistani side of the border.