Sudan's President Omar al-Bashir has issued a decree appointing new members of the former southern rebel movement to the national unity government.
The ministers are due to be sworn in shortly under the terms of a 2005 peace deal that ended the 21-year civil war.
The southern ministers left the government in October but most differences have now been resolved.
Recent clashes between southern forces and pro-government militiamen have reportedly left 100 dead.
The fighting in Bahr el-Gazal has now stopped.
Southern leader Salva Kiir said the militiamen "were acting under local commanders only... the situation is now under control."
The continued presence of northern militias in the south was one reason why the ex-rebel Sudan People's Liberation Movement pulled out of the national government in October.
They will be withdrawn soon and other issues have also been resolved.
However, the demarcation of the disputed oil-rich Abyei region has still not been settled.
Salva Kiir (l) and President Bashir (r) met to end the dispute
The SPLM's Deng Alor replaces Lam Akol as foreign minister, while other former rebels are to take up senior jobs.
The BBC's correspondent in Khartoum, Amber Henshaw, says many people feared Sudan was on the verge of sliding back into the brutal 20-year civil war that ended in 2005 and cost the lives of 1.5 million people.
But the SPLM agreed to end its boycott after its leader Salva Kiir met Sudanese President Omar al-Bashir.
The unity government will also set up a development commission to speed up road links between the more developed north and the south, which has little infrastructure after the long war.
Under the peace deal, the SPLM leader is also national vice-president.
There are currently 10,000 UN peacekeepers in South Sudan.