The performance of the #1 Audi was good during the second half of the race, but Audi had to double stint their tires to keep on fighting for the second place. This allowed them to spend a total time in the
pits of only 7:28.588, compared to 8:19.833 for the first placed #8 Toyota and 8:14.191 for the third-placed #7 Toyota.
The #8 Toyota was in another world performance-wise. The second-placed Audi finished 1:13.926 behind the Audi even though it spent approximately 50 seconds less in the pits than the #8. That means more than 2 minutes lost on track !
Looking at the performance during the race, Toyota should have been able to clinch a second 1-2 finish at Spa, but Wurz made a few costly errors on the #7 which also helped the #1 Audi.
It could be that Audi were trying a few things at Spa in terms of fuel consumption in order to reduce that lap stint deficit that they have compared to the competition, but if that's the case, they were probably compromising performance too much.