The men turned themselves in to security authorities and met Fourth Army commander Udomchai Thamsarorach at the Islamic Committee Office in Narathiwat.
The defectors participated in rebel movements in Si Sakhon, Rueso and Rangae districts of Narathiwat.
They face either security or criminal law charges, while others are charged under both laws.
Muktar Zeekaji, spokesman of the Prachatham Party, helped arrange for the men's surrender.
The defectors belonged to the rebel group calling itself Badan Penyelarasan Wawasan Baru Melayu Patani.
One of the defectors was Waeali Copter Waji, alias Jeh Ali, a key suspect in connection with the Jan 4, 2004 arms robbery at the 4th Development Battalion in Cho Ai-rong district in Narathiwat.
The men presented the army commander with a letter declaring they have formally quit the insurgency.
The letter said they believed the group's goals were too ambitious and its strategies were not achieving results.
The rebel group also changed its stance as the government shifted its security policies, the letter said.
Mr Muktar said that for the men, life in the forest hideouts was tough.
After a while, he said, they realised they were fighting a lost cause and decided to defect.
The defectors asked Gen Udomchai how the security officials intended to help them deal with the legal charges against them.
They said they wanted jobs and peaceful and safe lives.
Deputy Prime Minister Yutthasak Sasiprapa said Prime Minister Yingluck Shinawatra has promised to secure them jobs and give them loans to restart their lives.
State agencies will also ensure they are treated fairly in the legal proceedings, said Gen Yutthasak, who added the 91 were moderate separatists.
Hard-core members of the group remain at large.
Mr Muktar said that hundreds more rebels were ready to surrender. Some who faced legal charges have fled to Malaysia and returned occasionally, but could not find work.
"Everyone wants to come out in the open and look after their families. But, above all, they want safety," he said.
"If the government can provide what they ask for, there will be many more defectors," Mr Muktar added.
The 91 defectors, however, are not the same people whom Deputy Prime Minister Chalerm Yubamrung recently claimed were planning to surrender.
A former insurgent leader, who was among the defectors but declined to be named, said victory for the group was nowhere in sight.
He said the group was becoming weaker and was unable to deliver attacks as frequently as before.
The attacks it managed to perpetrate were symbolic, aimed mainly at making the group's presence felt, he added.
Separatist rebels had sincerely tried to fight for improved living conditions for people in the deep South, he said. But they soon became disenchanted.
"Many years have passed, we got nothing in return. We harmed the villagers who protected us. The fight came back to destroy us and destroy our hopes," he said.
Another defector said he wanted to quit the group after he became ill from prolonged exposure to chemicals used for making bombs.
He said he was hospitalised for a month.
"Then a thought came to me. Why do I waste my life away like this? No one in the separatist group visited me in hospital."
He said he now wanted "a place to stand in society, like everyone else".
Lt Gen Udomchai said he discussed peace with the defectors yesterday.
Army chief Gen Prayuth Chan-ocha said he thought the men surrendered because they had witnessed enough atrocities from violence.