He will no doubt be remembered as a misguided patriot who backed the wrong horse - the junta - against the Americans and Aristide, who returned to Haiti in glory once the generals had fled.
But Jonaissant in fact played a key role in sparing his country what would have been a swift but bloody US invasion on the night of 18-19 September 1994.
Jonaissant was born in the north-western town of Port-de-Paix. He studied Greco-Latin culture and was elected Haiti's youngest-ever senator at the age of 37 in 1950, before the years of the Duvalier dynasty. He was little- known during the Duvalier years, working as a classics professor, a judge and eventually a Supreme Court justice.
After the younger Duvalier, Jean-Claude ("Baby Doc"), was forced into exile in February 1986, Jonaissant was appointed by the interim military ruler Lt-Gen Henri Namphy as President of the Constituent Assembly that drew up a new constitution in 1987. He then served in the State Council, a body of wise men that helped guide Haiti towards new elections in 1990, won by Aristide. When Lt-Gen Raoul Cedras, leader of the 1991 coup that toppled Aristide, appointed Jonaissant provisional President of Haiti on 11 May 1994 - an appointment never recognised abroad - it was precisely for his honourable reputation, to give the generals an air of legitimacy. Angered by US threats of intervention, the "President" grew into the nationalistic role which led to his being branded a traitor by the Aristide camp.
Not everyone agreed. Opponents of Aristide were delighted when, in a rambling Creole speech in the small hours of 11 June 1994 - sprinkled with voodoo references - the de facto President declared a state of emergency and asked Haitians to fight to the death against any American intervention. "If they thought we had an atomic bomb, they would respect us. Haiti does not have an atomic bomb but it has better protectors than that," he said, in a clear reference to voodoo spirits.
Jonaissant was, in fact, known to Haitians as "Agaou", the name of a voodoo God, because of his habit of using the phrase "if Agaou wills . . .".
For one brief moment, at nightfall on Sunday 18 September 1994, Jonaissant was the focus of world attention. The US negotiators Jimmy Carter, General Colin Powell and Senator Sam Nunn had failed to persuade the junta to step down. President Bill Clinton ordered an invasion to begin. US paratroopers were in the air.
In a last-minute gamble, the three Americans went to the Presidential palace and cut a deal with Jonaissant - even though he was never recognised as President - under which the generals would leave. The invasion became a peaceful occupation the following morning.
"When he realised his countrymen were going to die, he singled-handedly stopped the invasion," said his long-time friend Aubelin Jolicoeur, a legendary Haitian who was Graham Greene's prototype for the character Petitpierre in the novel The Comedians. "He was the most honourable man I ever met. The fate of great men is to do great things without being recognised."
Emile Jonaissant, teacher, lawyer, politician: born Port-de-Paix, Haiti 1913; President of Haiti May-October 1994; died 24 October 1995.