With a maximum stint time of 65-minutes, a miscalculation saw the Mercedes dive into the pit lane too early, and was forced to hold Raffaele Marciello in the pits in order not to exceed the maximum stint.
It proved enough to drop the car to third, leaving Audi (Christopher Hasse, Markus Winkelhock and Jules Gounon) an unrivalled run to the flag in the final hour.
Bentley recorded second place with the battle-scarred #8 Team M-Sport entry while the #117 KUS Team75 Bernhard Porsche took fourth.
It was a race that promised more for Porsche, the #117 car having served a three-minute penalty earlier in the race after hitting a rival mechanic while exiting the pits, along with a drive through for exceeding track limits.
Without the penalties, the Porsche would have been much higher and showed pace strong enough to have won the race had it not struck trouble.
Dominating the first half of the race, the #55 Kaspersky Ferrari dramatically crashed out at Eau Rouge.
That followed contact with the #90 Mercedes, driven by Marciello, at La Source, damaging the Ferrari's steering and sending driver Marco Cioci skidding into the tyre barriers at Eau Rouge moments later.
The #90 car sat in second place at the time, and was looking to lap the #55 as strategy and rain saw them temporarily a lap apart.
For the first half of the race the top half dozen shared the same lap, with little to separate them outside of their respective pit cycles.
Once dawn broke, the race had begun to fracture, with the #90 Mercedes heading the race from the #1 Audi Sport WRT entry and Team M-Sport's #8 Bentley.
Having enjoyed a long stretch of green flag racing to start proceedings, full course yellows and safety cars punctuated the race from the three-hour mark when the #50 Ferrari crash heavily at Eau Rouge.
A raft of other cars also found met an early demise, with almost half of the 63-car field failing to see the chequered flag.
Their task wasn't helped by a brief period of rain during the night, which shook up the order at a time when teams were beginning to serve their compulsory five-minute technical pit stop.
It proved to be a net gain for those who took the opportunity to stop while the rain fell, with the relative pace of those on track slower compared with those who'd completed their technical stop under dry conditions.
The final hours saw a nail-biting battle between the #25 Audi and #90 Mercedes, with positions changing throughout as the pair stopped off sequence.
Ultimately, it was Audi which had the better strategy, winning by just 13-seconds from Bentley and the #90 Mercedes some 38-seconds further back.
The #16 Black Falcon Mercedes claimed the Pro-Am class while the Kessel Ferrari wrapped up the Amateur class with the #888 entry.