The Navy said it was moving training operations to Florida and elsewhere in the US.
Local protesters say the move is a victory for their campaign against the live-fire exercises which first began in 1947, but the Navy said the decision was not influenced by public pressure.
The issue made headlines in 1999 after a stray bomb killed a civilian guard.
Ideal terrain
Lieutenant Commander Kim Dixon, a Navy spokeswoman, confirmed that the exercises on Vieques were over and that the warships involved would continue training at sea.
"The training overall went very smoothly," she said. "They accomplished all their missions."
Shells fired from the guided-missile cruiser USS Ticonderoga on Saturday marked the island's final use as a test range.
Puerto Rico has US commonwealth status, and the island was seen by US military planners as ideal terrain for training in amphibious operations.
'Forced out'
Protesters on Vieques drove in a convoy of about 100 cars through civilian areas this weekend, honking horns to celebrate the end of the exercises.
"The Navy is not leaving because it wants to but because the people have forced them out," protest leader Nilda Medina said.
Campaigners accuse the Navy of polluting the island and damaging the health of its 9,100 inhabitants - a claim the Pentagon rejects.
Since 1999, more than 1,000 protesters have been arrested for trespassing on Navy land.
The Navy will actually remain on Vieques until 1 May when it turns over the eastern third of the island to the US Department of the Interior.