Condor Ferries will sail from Poole from Friday following the delivery of a £50m, 102m (335ft) vessel, which is too big for Weymouth's port.
Weymouth and Portland Borough Council spent £4.5m rebuilding its ferry berth after it began to collapse in 2012. It reopened less than two years ago.
It is estimated the move will cost Weymouth Harbour about £750,000 a year.
The final ferry left at 13:30 GMT and will return at 22:30.
Condor Ferries returned to Weymouth in July 2013, 18 months after huge cracks appeared in the 80-year-old ferry berth.
The operator temporarily moved services to Poole while the harbour wall was repaired but, a year later, announced plans to buy a bigger vessel for its Channel Islands service, meaning the Weymouth berth required a further £10m worth of work.
Pleas by the council and South Dorset MP Richard Drax for government funding were unsuccessful and Condor announced it would instead use the existing berth at Poole.
The new larger ship replaces two smaller vessels, which have been sold to Greek firm Seajets.
It can carry up to 880 passengers and 245 vehicles.
The current fast ferries each have capacity for up to 741 passengers and 175 vehicles.
Cross-channel ferry services from Weymouth have come to an end with the final sailing to Guernsey.