It has not been smooth sailing. Only a few days into the talks – a fortnight ago – the prospect of peace was further threatened as the government rejected the rebels’ demands for amnesty and inclusion in a new unity government.
The armed groups say immunity will encourage the laying down of arms but critics say the real aim is to avoid prosecution at the International Criminal Court (ICC).
The chairman of the AU Commission Moussa Faki welcomed the agreement, saying he was happy for the people of the Central African Republic.
It is this population who have borne the brunt of the conflict, with an estimated 2.4 million people in need of humanitarian assistance.
It is now likely that many of those who caused their predicament will not be held responsible.
Some elements of the anti-Balaka might also feel like they have not benefited as much, having been the only rebels publicly targeted so far by the ICC Prosecutor Fatou Bensouda.
The parties involved in this deal will have to work against a poor recent record in which there have been up to seven previous failed attempts at peace agreements since 2013.
The rebel groups still control large parts of the country and their presence is unlikely to be challenged now.
Opposition parties were not involved in the talks and they will move further down the political pecking order as the rebels get more involved in government.
Previous attempts by the AU to broker talks in Bangui, the capital of CAR, came to nothing.
While it worked with the UN as the mediators of this round of talks, the process in Khartoum was actually kick-started by Russia – which has been increasingly involved in the CAR in recent years.
Moscow has mining interests in the African nation and provides security for President Touadera.
Sudan, the host of the talks, will be hoping that the current success of the negotiations will improve its image, having been diplomatically and economically stranded for years.