Seven-times world champion Lewis Hamilton qualified fifth at Yas Marina, dimming hopes that he might avoid a first season without a win, while teammate and last weekend's Brazilian Grand Prix winner George Russell will line up sixth on Sunday.
"Today, I just heard, is World Toilet Day so I think that is one to put in the toilet," Wolff told Sky Sports television.
"I think we didn't get the job done. I think we went backwards and they (Ferrari) did a little step forward," added the Austrian.
"We went on a high-downforce, high-drag concept in order to have a good race car tomorrow and that was just so slow on the straights."
With Max Verstappen and Red Bull having clinched both titles already, Mercedes and Ferrari are fighting for the runner-up slot in the constructors' championship.
Mercedes, winners of a record eight constructors' titles in a row until Red Bull dethroned them this year, are 19 points behind Ferrari.
The Italian team had Charles Leclerc and Carlos Sainz qualify third and fourth, with Verstappen on pole and Red Bull teammate Sergio Perez alongside him on the front row.
Hamilton said Mercedes had thought Abu Dhabi would be a difficult track for them but he had not been expecting such a margin, with the Briton nearly eight-tenths off Verstappen's pole pace.
"Six-tenths of that is just on the straight," added Hamilton, a five-times winner at Yas Marina.
"Bouncing is back, with a vengeance. And that's definitely losing us time."
Mercedes spent much of the early part of the season battling 'porpoising', the bouncing on the straight that they appeared to have fixed in recent races.
Hamilton said there had also been a brake problem with the discs.
"When you hit the brake the car pulls one direction. Going into turn five, the car's pulling to the right and it's a left-hand corner so it's not ideal," he said.
