The five fugitives were expected to hand in a list of foreign militants living with them in South Waziristan.
Thousands of turbaned Pashtun tribesmen looked on as the five men from the Zallikhel tribe turned themselves in before a "Jirga", or tribal council, and pledged loyalty to Pakistan in return for clemency.
In Shakai, a remote village around 400-kilometre south-east of Islamabad, the surrendering men gave traditional peace offerings of garlands, turbans, pistols and swords to the army officers.
Director General ISPR, Major General Shaukat Sultan, IG Frontier Corps, Major General Hamid Khan, GOC Kohat, Major General Niaz Khattak, Secretary Fata, Brigadier Mehmood Shah (Retd) and other high ranking officials were present at the occasion.
Those who handed themselves over to authorities were Maulana Nek Mohammad, Haji Sharif, Noorul Islam, Maulana Abbas and Gul Hassan on behalf of Maulana Abdul Aziz.
"We give amnesty to these people in return for their pledge of brotherhood and loyalty," said Corps Commander Peshawar, Lieutenant-General Safdar Hussain, who arrived at the Jirga amid chants of "Allah-o-Akbar."
He said the foreign militants had until April 30 to surrender and receive a pardon or he would send troops after them.
Safdar Hussain also announced the release of 50 tribesmen arrested after fierce clashes with Pakistani forces last month.
Amid loud applause from tribesmen famous for their independence from state authority, the leader of the five declared his allegiance.
"Pakistan is our home. We want peace here. The Pakistani forces are our brothers," Nek Mohammad said. "We regret for what has been done on the basis of misunderstanding."
Under terms brokered by local MNAs, Nek Mohammad's band faced a choice of surrendering or expulsion from their homeland in the semi-autonomous region of Pakistan's North-West Frontier Province.
Pakistan has 25 senior al-Qaeda and Taleban suspects on its wanted list. But it has offered to let other foreign Mujahideen, who have made homes with the tribes during the past two decades, stay on so long as they register their presence.
Many Arab and Central Asian veterans of the war against the Soviet occupation of Afghanistan, who later backed the Taleban, married into families of tribesmen they had fought alongside.
US Lieutenant Colonel Matt Beevers told a news briefing in Kabul he welcomed the negotiated settlement in Shakai but military action was still likely to be needed.
"At the end of the day, I think we expect some Pakistani action there. They've done it in the past and I think they will continue to do it," Beevers said.
Our Peshawar correspondent adds: The Director General Inter-Services Public Relations (ISPR), Major General Shaukat Sultan said on Saturday that the five most wanted tribesmen of Zallikhel tribe have given up militancy and decided not to harbour foreign terrorists and will remain loyal to the country.
He was briefing newsmen about the reconciliation reached with the wanted tribesmen during a big traditional tribal Jirga in Shakai area of South Waziristan Agency.
Shaukat Sultan said that in the aftermath of the Wana operation, a tribal Jirga comprising of all sub-tribes of the Ahmadzai Wazir tribe along with two MNAs from the agency, the political administration and the military have reached on a political resolution of the matter to end militancy with the wanted tribesmen presenting their personal arms to the Corps Commander Peshawar.
The DG ISPR said the wanted tribesmen have assured good conduct in the future and would not indulge themselves in activities detrimental to the interest of the country. He said, tribesmen are brave and respected people and their decision to reconcile with the situation would in no way mean any let up in war on terrorism.
He said foreign elements hiding in the tribal belt have been given April 30 deadline and now they have with no other option than to surrender or quit our territory. "There is no third option available with them," Shaukat Sultan explained.
Replying a query, the spokesmen of Pakistan army clarified that the agreement has been reached with the local wanted tribesmen as they have realised now that whatever happened in Wana was a result of misunderstanding and now it is the matter of past.
To a question, he said, the army will remain deployed in the area to ensure elimination of foreign nationals and will also step up developmental activities in the Shakai valley of the South Waziristan.
"Out of 163 arrested tribesmen in the wake of various operations in Wana, fifty, who have been declared innocent after the interrogations, will be set free on Sunday (today)," he informed in response to a question
When asked about the agreement with the wanted elements, DG ISPR said, we could not compare them with the criminals as after every conflict there is agreement for peace. And this agreement was meant to do away with the conflict, he explained.