The signing ceremony on Friday was accompanied by singing and cries of joy.
The conflict has killed an estimated two million people, mainly through famine and disease and uprooted another four million.
The two protocols were signed in the presence of Sudanese President Umar Hasan Ahmad al-Bashir, his South African counterpart Thabo Mbeki, and Kenyan Vice-President Moody Awori.
The protocols grant the south the right to self-determination after six years of self-rule, power and wealth-sharing, management of national security and administration of disputed regions in the centre of the country during the post-conflict interim period.
The accords signed in Naivasha do not cover a separate conflict in Sudan's western Darfur region, where more than a year of fighting has created what the UN says is one of the world's worst humanitarian crises.
But diplomats believe a north-south deal could be a blueprint for peace in Darfur.
The US announced it will help Khartoum and southern Sudanese rebels in implementing the peace deal they signed in Kenya on Friday.
Powell said the deal could be a
blueprint for peace in Darfur
"The United States will strongly support implementation of the peace agreement, that will commence following the 9 January signing ceremony, in order to promote stability, prosperity and democracy in a unified Sudan," US Secretary of State Colin Powell said.
His statement was released at UN headquarters in New York as he arrived there for a meeting with UN Secretary-General Kofi Annan on mobilising relief for tsunami victims.
"We are firmly committed to normalising our relationship with the new government that will be formed as a result of the north-south accord and to assisting with reconstruction and development, but this can only take place with a Sudan that is at peace, with the peace process being implemented throughout the entire country," Powell said.
Powell added that carrying out the terms of the Naivasha accord would send a message to the parties in the Darfur conflict - and throughout the world - that "the most intractable of conflicts can be resolved," he said.
"We expect all the parties to work together decisively and immediately to end the violence in Darfur," Powell said.
"There are two tracks, but they must lead to the same point - peace, stability, and prosperity for all of the people of Sudan."