Boni Yayi left on Saturday after "his health deteriorated rapidly", Noureni Atchade, spokesman for his Cowry Forces for an Emerging Benin (FCBE) party, said in an interview with Radio France Internationale, without giving details.
The former leader's surprise departure came after weeks of tension with President Patrice Talon, that saw Boni Yayi confined to his northern Benin home.
Protests first erupted in Benin after April 28 parliamentary elections. Several people have died in clashes with police who resorted to gunfire.
The crisis has stoked concerns of an authoritarian turn in a country once seen as a democratic example in the region.
The voting took place without any opposition candidate, and all 83 members of parliament now come from the only two parties allowed to take part, both allied to Talon.
Changes to electoral rules had effectively barred opposition parties from fielding candidates.
The demonstrators had demanded the lifting of a police cordon around Boni Yayi's house in the country's economic capital Cotonou.
The former president left the country without giving an explanation to the authorities, the party spokesman said, while stressing that he was not evading justice.
On Sunday morning, a source close to Boni Yayi said he had arrived in Togo's capital Lome, without giving further details.
'War of egos'
In early June, Boni Yayi had received a court summons but his lawyers had refused due to his health problems and the stress of his home being surrounded by security forces.
The republican police on Saturday announced that Cadjehoun, the district of Cotonou where Boni Yayi's house is, was "free of any police presence" following negotiations between Talon and traditional leaders and officials from Save and Tchaourou, Boni Yayi's hometown.
Talon on Friday said he had "taken steps" to resolve the political crisis.
"I do not have a personal problem with Boni Yayi," Talon said, adding he was "a friend".
Most high-profile opponents of Talon now live in exile, fearing legal action against them if they return.
Boni Yayi had been seen as a symbol of opposition staying put in the country. He had denounced an "electoral coup" following the April polls, calling for the results to be annulled and for the people to rise up.
"The socio-political life of Benin has for a few years been a prisoner in the war of egos between two individuals: Patrice Talon and Boni Yayi," said political scientist Expedit B. Ologou, president of the CiAAF analysis centre, based in Cotonou.
When Boni Yayi was president (2006-2016), Talon was himself forced into exile between 2012 and 2015, accused of "attempted poisoning" against the head of state.
However political analyst Gilles Yabi, founder of the Wathi think tank, said "it would be simplistic to think that the political crisis in Benin is a fight between two men."
"There seems to be a systematic and methodical plan to control the institutions and the political scene of the country," he told AFP.