Defending race winner Vanthoor was sharing the #47 KCMG Porsche 911 GT3 R with Nick Tandy and Maxime Martin.
However, just beyond the 16-hour mark, Porsche announced that Vanthoor had been forced to withdraw from the remainder of the race, leaving team-mates Tandy and Martin to complete the race as a duo.
Vanthoor subsequently tweeted that he had been knocked over by a quad bike in the paddock while riding his scooter.
The Belgian racer added: “I landed heavily on my head and have multiple wounds in my face. I’m doing fine but currently at the hospital for further checks and stitches.”
Vanthoor’s withdrawal comes as another blow to Porsche’s hopes of winning the Spa 24 Hours for a third year in a row, with Tandy and Martin currently circulating a lap down in fifth place.
The #51 Iron Lynx Ferrari 488 GT3 of Alessandro Pier Guidi, Come Ledogar and Nicklas Nielsen continue to lead the way with a little over eight hours of the race left to run.
Both the #51 crew and their nearest pursuer, the #32 Team WRT Audi R8 LMS GT3, were able to serve their mandatory four-minute ‘technical pitstop’ during a full-course yellow period in the 16th hour triggered by an off for the #16 Grasser Lamborghini Huracan GT3.
KCMG Porsche will run to the end with Martin and Tandy alternating
Photo by: GTWCE
A subsequent safety car period however has closed the gap between the two leading cars, with Nielsen circulating around six seconds clear of the WRT Audi of Kelvin van der Linde.
The Garage 59 Aston Martin Vantage GT3, which served its technical pitstop under green flag conditions just after the halfway mark, is the only other car on the lead lap in third place with Ross Gunn at the wheel.
One of the contenders for victory, the pole-sitting #88 ASP Mercedes-AMG GT3, dropped out of the race around the 16-hour mark due to a broken left-rear damper.
Jules Gounon had been lapping within a couple of seconds of the pace despite the issue before it became too severe to continue.