Although the main faction of the rebel Sudan Liberation Movement signed the May 5 peace with the Khartoum government, a splinter faction held out until Thursday.
So did the south Darfur faction of the Justice and Equality Movement.
"We shall be bound by the letter and spirit of the [Darfur Peace Accord] and shall assume and implement the relevant obligations therein, especially those related to the comprehensive ceasefire agreement," the letter said.
Said Djinnit, the African Union peace and security commissioner, said after the signing ceremony in Addis Ababa that "the former holdouts should do their utmost to urge their respective members and fellow Darfurians to join the peace process".
Decades of low-level clashes in Darfur over land and water erupted in early 2003 when rebel groups of ethnic Africans rose up against the Arab-led government in Khartoum.
The government is accused of responding by unleashing Arab militias known as the janjawid, who have been accused of sweeping atrocities against the African population. Khartoum denies any involvement.
The three-year Darfur conflict has claimed at least 180,000 lives and forced more than 2 million people to flee. One key provision in the accord calls for the protection of civilians in the vast western region.
The UN, AU and aid groups have said violence has worsened since the accord was signed, as armed groups try to secure more territory ahead of implementing a ceasefire.
It could be months before a UN force is in place.