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.
The school he founded is believed to have incubated many rank-and-file rebels.
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"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.
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.
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.
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