By Agence France-Presse
Sapae-ing established a leading Islamic school and became a folkloric figure for many Malay-Muslims in Thailand's culturally distinct far south despite being in self-exile since 2004.
The insurgency sees separatist rebels carry out near-daily attacks on security forces and perceived collaborators with the Thai state, which colonised the region over a century ago.
The majority of the dead are civilians in a conflict that has seen both insurgents and Thailand's military accused of rights abuses.
Sapae-ing, who was in his eighties, died peacefully on January 10 across the Thai border in Malaysia where he had lived since fleeing treason charges.
The school he founded is believed to have incubated many rank-and-file rebels.
"He was a philosopher who played an important role in education," said a statement by the Mara Patani, a group representing some rebel factions in peace talks with the Thai junta, confirming his death.
Mosques have been packed across the south for special prayers since his death was confirmed.
Thailand-based security analyst Don Pathan said his schools became "pillars of Malay identity" drawing the ire of Thai authorities as the insurgency gathered pace.
"He was a Yoda-like figure.. he had a mystique," Pathan said, explaining that Sapea-ing's profile grew through the 1980s and 90s as he "spoke up for Malay identity and refused to bow down to the Thai state".
Thailand's military elite have long been accused by the kingdom's minority groups of enforcing a centralised concept of "Thainess" at the expense of diversity.
In the Malay-speaking south, for example, Thai language and script has been enforced for decades, fuelling anger and resentment.
Sapae-ing's legend grew across the unrest-hit southern states despite his relative silence in self-exile.
Zachary Abuza, a specialist on Southeast Asian militant groups, said he had a galvanising role in the rebellion -- although his operational links with rebel foot soldiers are unknown.
"This is a movement with almost no known leadership. He was as close as it got... being on the run for 13 years gave him a bit of a Robin Hood status."
An end to the fighting remains distant despite peace contacts.
The armed insurgents, dominated by the publicity-averse Barisan Revolusi Nasional (BRN), want an amnesty for their operatives and serious discussion on devolution, leading to independence.
The Thai junta remain coy on ceding powers and do not believe the rebel groups they have command-and-control over the militant foot soliders.