The Black Falcon Mercedes squad topped the times in first qualifying for the Spa 24 Hours ahead of the superpole session that determines the first 20 places on the grid.
Factory drivers Maro Engel, Yelmer Buurman and Luca Stolz claimed the provisional pole for the blue-riband Blancpain GT Series round in the aggregate session on Thursday evening with a 2m19.750s average aboard their Mercedes-AMG GT3.
Buurman, who set the quickest lap of the multi-part session with a 2m19.231s, said: "The most difficult part is getting a clear lap with 72 cars on track.
"The team did well to put me out on track at the right time and from then on it was about doing what you like doing — pushing really hard. It was a good, fun lap, but this session is maybe not about pushing for the last tenth."
Vanthoor set the second fastest qualifying lap across the sessions aboard the best of the factory WRT Audi R8 LMS GT3s. He posted his 2m19.238s on the opening run for the car, despite the fuel load being at its heaviest.
Bentley just missed out on a place in the superpole runs on Friday. Best of the four-strong fleet of factory M-Sport Continental GT3s was the car shared by Jordan Pepper, Steven Kane and Jules Gounon in 21st position.
BMW, winner of the Belgian 24-hour classic last year, also failed to get a car through into superpole.