The St. Johns River Ferry has carried passengers from Mayport to St. George Island and back since 1894.
The ship is now under control of new operators.
The Jacksonville Port Authority handed control over to the St. Johns River Ferry Commission on Sunday night at a ceremony in Mayport.
The final crossing under JaxPort's control carried dozens of ferry supporters who used a grassroots effort to keep the ship afloat.
"It would have been a significant ride for people to come in from (Interstates) 95 and 295, then go all the way out. And they probably would have bypassed all of Jacksonville Beach, Atlantic Beach, Neptune Beach and Ponte Vedra. It's significant in economic development and jobs," said Elaine Brown, a member of the St. Johns River Ferry Commission.
JaxPort decided earlier in the year it can no longer afford to operate the ferry and is turning over its operation to a nonprofit St. Johns River Ferry Commission on Oct. 1. JaxPort and the city of Jacksonville have each pledged $200,000 to the commission, but that is not enough money to run the ferry for the year.
The ferry will continue to operate on its normal schedule.
Riders will see an increase in fares. Cars will now pay $6 and motorcycles will pay $5. Frequent riders who purchase tickets by getting coupon books good for 20 crossings would pay $80, up from $60.