The peace deal is expected to end a conflict that has been simmering in the former tourism hotspot for over two decades.
"All the conditions are present today to have a definitive accord," Interior Minister Osman Ngom, who signed the deal for the government, said in the province's capital Ziguinchor on Thursday.
"It has been meticulously prepared by both sides."
Under the accord, the rebels have declared their armed struggle over and agreed to lay down their weapons, although there is no time-frame for disarmament.
Father Diamacoune Senghor, a 76-year-old Catholic priest who is the historic leader of the Movement of Democratic Forces of Casamance (MFDC), signed the deal for the rebels, whose movement has been undermined by internal divisions.
One small rebel faction refused to take part in the signing ceremony, which was also attended by opposition and religious leaders as well as thousands of ordinary Casamance residents.
Ngom played down the significance of the no-show.
"All the conditions are present today to have a definitive accord"
Senegal Interior Minister
"What is important is that the government's partners in the accord are credible and determined," he said.
The MFDC has fought a low-level insurgency for greater autonomy in the largely Christian and animist region since 1982.
Hundreds have been killed.
While the worst violence in Casamance, one of Africa's longest conflicts, ended in the 1990s, sporadic gun battles have continued in the region, which is still littered with landmines.
Senegal's President Abdoulaye Wade, who was elected in 2000, has made peace in Casamance - cut off from the rest of the country by tiny Gambia - one of his top priorities.
Earlier this year, he said the end of the conflict was close and announced an amnesty for the rebels.
Senegal, which stands out as a haven of stability among its turbulent West African neighbours, wants to return Casamance to its past fortunes as the country's bread basket and attract tourists back to its white beaches and lush mangrove swamps.