Weather and track conditions changed over and over, as the nr 50 Freisinger Motorsport Porsche 996 GT3-RS and the nr 1 Larbre Competition Chrysler Viper swapped the lead several times. From 22:00 to 04:00 a lot of cars ran into technical problems or visited the gravel traps, while the safety car showed up three more times. But the biggest news was the official retirement of the nr 23 BMS Scuderia Italia Ferrari 550 Maranello, due to engine problems. This stopped the winning streak of Matteo Bobbi and Thomas Biagi who had won all the first five rounds of the Championship.

At mid race, 34 cars were still running. The nr 50 Porsche of Ortelli, Lieb and Dumas was leading the race and the N-GT with a margin of 90 seconds ahead of the first of the GT class, the nr 1 Chrysler of Bouchut, Huisman, Vosse and Dumez. 

At the end of the third safety car period, the nr 50 Freisinger Motorsport Porsche was still leading both the overall classification and the N-GT Class. At 22:30 BMS Scuderia Italia officially retired their nr 23 Ferrari 550, which had been in the pits for some time due to engine problems. The fight for the lead intensified, as the nr 1 Larbre Competition Chrysler Viper and the nr 9 JMB Racing Ferrari 550 were chasing the leading Porsche. A few minutes before the seventh hour expired, the nr 68 Peter Kutemann Ferrari 360 crashed at the Raidillon and retired. This accident brought the safety car out for the sixth time.

The race resumed half an hour later, still under heavy rain. Five minutes after midnight the nr. 73 Seikel Motorsport Porsche, which was 10th in the N-GT Class, came into the pits and retired because of a technical problem. Just afterwards the nr 84 T2M Motorsport Porsche went off into a gravel trap, and the safety car reappeared for the seventh time. The neutralization lasted only 15 minutes and the race restarted at 00:27. The following hour was relatively calm: the rain had stopped and the drivers were very cautious on the slippery track. Then, at 01:35, the nr 6 Creation Autosportif Lister Storm and the nr 67 Autorlando Sport Porsche collided at Blanchimont. Bobby Verdon Roe managed to get back to the pits at the wheel of the British car, despite extensive damage. On the contrary, Marco Facchetti’s Porsche stopped on the track, and the safety car intervened for the eighth time to retrieve it.

The green light restarted the race at 02:06. Eight minutes later, race leader Christophe Bouchut came back into the pits in his nr 1 Larbre Competition Chrysler Viper; the crew changed the windscreen wiper and fixed the bonnet with bands of adhesive tape. The weather changed to drizzle and the nr 5 Force One Chrysler Viper was given a drive-through penalty because a mechanic changed the windscreen wipers during the refuelling; the car was lying in 9th position overall and 5th in the GT Class. This was the beginning of a series of stops due to electrical and transmission problems. The nr 89 TMC Ferrari 360 was also in trouble, and came into the pits to change the gearbox.

Despite intermittent light rain, the racing lines were drying. Twenty minutes before the end of the 11th hour, some cars pitted for slick tyres, including the leading nr 50 Freisinger Motorsport Porsche. The nr 1 Larbre Competition Chrysler Viper took the lead again, but it was still on rain tyres and this enabled the nr 50 Porsche to reduce the gap by several seconds per lap. The nr 1 Chrysler pitted again for slick tyres at 03:07, and this resulted in the 15th lead change with the nr 50 Porsche back in command. At the wheel of the nr 17 Larbre Competiton Chrysler Viper, Vanina Ickx emerged as the fastest driver with slick tyres on the damp track, and recovered several positions. 

At 03:23 the nr 5 Force One Chrysler Viper stopped at the Eau Rouge, then rejoined and came back into the pits with gearbox problems. At 03:30 two cars went off the track and remained stuck in the gravel traps almost at the same time. The nr 74 Team Eurotech Porsche at Stavelot, the nr 61 EMKA Racing Porsche at Rivages. Both cars rejoined after a few minutes, but the nr 61 Porsche lost the third position overall and dropped down to 10th. Rain intensified again as the first half of the race was expiring. 

At 04:00, after 12 hours of racing, the second allocation of Championship points took place.  Larbre Competition claimed 6.5 points in GT, with Lister Racing adding 2.5 to their score.  However, both BMS Scuderia Italia and the Bobbi/Biagi duo still have a healthy lead.  In N-GT, maximum points for the nr 50 Freisinger Porsche increased the Championship lead of Ortelli and Lieb.