After nearly six hours of work, the 800-kilogram (1,800-pound) cetacean was lifted from the river by a net and crane at around 4:00 am and placed on a barge under the immediate care of a dozen veterinarians.
The beluga, a protected species usually found in cold Arctic waters, will next be placed in a refrigerated truck and transported to the coast, Isabelle Dorliat-Pouzet, secretary general of the Eure prefecture, said ahead of the rescue operation.
The four-metre (13-foot) whale was spotted more than a week ago heading towards Paris and was stranded some 130 kilometres (80 miles) inland from the Channel at Saint-Pierre-La-Garenne in Normandy.
Since Friday, the animal's movement inland has been blocked by a lock at Saint-Pierre-La-Garenne, 70 kilometres northwest of Paris, and its health had deteriorated after it refused to eat.
But its condition was "satisfactory", Isabelle Brasseur of the Marineland sea animal park in southern France, Europe's biggest, told AFP earlier on Tuesday.
A seawater basin at a lock in the Channel port of Ouistreham has been readied for the animal, which will spend three days there under observation in preparation for its release.
The "exceptional" operation to return it to the sea is not without risk for the whale, which is already weakened and stressed, said Brasseur, part of a Marineland team sent to assist with the rescue, alongside the NGO Sea Shepherd France.
"It could be that he dies now, during the handling, during the journey or at point B," in Ouistreham, she said.
The 24 divers involved in the operation and the rescuers handling the ropes had to try several times between 10:00 pm and 4:00 am to lure the animal into the nets to be lifted out of the water.
A handful of curious people remained on the bank all night to observe the operation.