The Italian had taken a brilliant pole position with a pole lap of 2m00.77s only to lose it for track limit violation at T7. As a result, Kobayashi slipped down to third, behind his team-mate Miguel Molina.
The #2 Cadillac V-Series.R entry driven by Earl Bamber went fourth, ahead of the sister car qualified by Sebastien Bourdais that joined the WEC grid this weekend.
Sixth was the best of the Porsches, the #6 official entry driven by Kevin Estre, with the customer car from Hertz Team Jota with Will Stevens aboard in seventh.
Oliver Pla in Glickenhaus Racing grabbed eighth and was the best-placed non-Hybrid Hypercar.
The #93 Peugeot 9X8 of Jean-Eric Vergne qualified ninth, ahead of the #5 Porsche 963 of Frederic Makowiecki, who rounded out the top ten.
The #8 Toyota GR010 did not post a time as Brendon Hartley crashed at Raidillon on his out lap. The points leaders will have to start from the rear of the Hypercar grid tomorrow.
The #23 United Autosports claimed the LMP2 class pole position as returnee Tom Blomqvist shone in the session with a rapid 2m05.979s best lap.
The British driver is yet to drive in a race this season after his car suffered a retirement at Sebring and he missed out on the Portimao round due to his IMSA commitments.
Second on the grid will be the #41 WRT Oreca-Gibson as Louis Deletraz was 0.3s off the pole. Prema Racing was third with #63 car with Daniil Kvyat behind the wheel.
Ahmad Al Harthy in ORT by TF Aston Martin clinched a sensational first pole position with a scorching 2m17.216s lap.
The Omani driver was entire 1.9s faster than second-placed Iron Dames Porsche driven by local ace Sarah Bovy.
Ryan Hardwick completed the best qualifying of the season for the #88 Dempsey Proton Porsche 911 RSR-19 and will line up in third position on the LMGTE Am grid.
The session was red-flagged after PJ Hyett in Project 1-AO Porsche 911 RSR-19 crashed at Raidillon.
