File Photo: Mercedes team principal Toto Wolff. AFP
He suggested the deposed champion would "never get over" the end-of-race decision-making that had left him a "sitting duck" for Max Verstappen.
And although he had yet to receive assurances that Hamilton would return next season for another tilt at an unprecedented eighth title Wolff stated: "As a racer his heart will say I need to continue because he's at the peak of his game".
Both Wolff and Hamilton are boycotting Thursday evening's gala dinner at the FIA's Paris headquarters.
"Both of us won't be there," the Austrian confirmed.
"I won't be there because of my loyalty to Lewis and because of my own personal integrity."
Mercedes lodged two appeals immediately after Sunday's dramatic finish where, after coasting to victory Hamilton suddenly found himself in a last-lap 'shoot-out' with Verstappen.
That arose after FIA race director Michael Masi ruled that the five lapped cars between Hamilton's Mercedes and Verstappen's Red Bull could unlap themselves.
It left Verstappen, who had pitted for fresher tyres, to streak past Hamilton and take the race win and his first title.
- 'will ever get over it' -
Those two appeals were rejected, with Mercedes then announcing their intention to lodge another appeal, which they withdrew on Thursday hours before the deadline.
"We believe we had a very strong case and if you look at it from the legal side if it would have been judged in a regular court, almost guaranteed that we would have won.
"But the problem with the FIA is the way it's structured, the FIA can't really mark their own homework.
"And there's a difference between being right and obtaining justice."
He added: "We decided together with Lewis to protest, to launch the appeal, and to withdraw the appeal.
"But you can imagine not only for him but also for us as a team it was terrible to be confronted with a decision that decided the outcome of the world championship.
"But neither him nor us wanted to win the world championship in the court room."
Wolff said Hamilton had the race in the bag, until the final four minutes of mayhem.
"He had a commanding lead in Abu Dhabi on Sunday from the get go.
"He won the start and he never gave the lead away again, and robbing him in the last lap of the race is unacceptable."
He said the ball was now in the FIA's court "to decide how to move forward so these decisions can be avoided".
Wolff suggested neither he nor Hamilton "will ever get over it".
"That's not possible, certainly not as a driver. But I would certainly hope that the two of us with the rest of the team we can work through the events, with the FIA and F1 and utilise the situation to improve the sport.
"But we will never overcome the pain and the distress that were caused on Sunday."
He was at pains to say Mercedes' appeals were not aimed at Verstappen and Red Bull, but the FIA's "random" use of the rulebook.
"This situation has nothing to do with Max.
"He is a worthy champion. his driving is exceptional and Red Bull are fierce competitors and I have the greatest respect for the people working there."
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