An alternative for many who can't afford the cost of a plane ticket, the maritime link is vital for the economy of the rural and cut-off Casamance region.
The service had been closed for nine months due to political unrest and the resumption overnight Tuesday to Wednesday coincided with celebrations marking the end of the Muslim holy month of Ramadan when many people return home.
"We are very, very happy because we suffered a lot during the nine months," said Astou Sane, a nurse, as she boarded.
"We were traveling by road, with (all) the works. When you get there, you've got flu, you're tired."
Some 233 passengers embarked on the Aline Sitoe Diatta ferry which sounded its foghorn while departing the port of Dakar after dark, according to ferry terminal official Oumar Samb and AFP journalists.
The vessel was less than half full due to the short notice given for the service's restoration, Samb said.
It was scheduled to arrive in Ziguinchor, the main city in Casamance, before midday (1200 GMT) on Wednesday. Ticket prices start at 5,000 CFA francs (7.6 euros, $8.3)
Alain Theophile Sane, a researcher in medical biology, said he'd booked a cabin.
"You can sleep during the journey. You arrive rested, all fresh.
"By road, the path is quite bumpy in places, you get there exhausted," he said.
Authorities halted the ferry service last June without any official explanation, fuelling suspicions they just wanted to punish the region.
It followed deadly unrest in Ziguinchor and other cities, sparked by the conviction of former opposition politician and now prime minister Ousmane Sonko.
Sonko grew up in Casamance and two years ago became Ziguinchor's mayor.
Popular and charismatic, he was barred from running in last month's presidential election after a string of legal convictions which he condemned as politically motivated.
Instead, he backed his political ally who is now Senegal's new President Bassirou Diomaye Faye.
'Under embargo'
The maritime link, operated by three ships, carries hundreds of passengers every week between the capital and Casamance, several hundred kilometers (miles) to the south, running along the Atlantic coast in both directions.
The service is also key for traders, tourists and students and for transporting freight, fruit and fish.
Casamance is almost separated from the rest of Senegal by the tiny state of The Gambia.
More than 5,000 people signed a petition organized in October by the head of a processing company for agricultural products over the impact of the ferry's suspension on jobs and income for thousands of families as well as on the price of goods.
Xavier Diatta said a large part of the mango crop had rotted and that producers of fish and cashew nuts also faced problems.
Pape Samba Cisse, a teacher, said on the pier that the ferry's return would be greeted by all Casamance residents with a "sigh of relief."
"We were put under embargo," he said.