Giovinazzi found two tenths on a second quick lap aboard his Ferrari 499P Le Mans Hypercar to leapfrog AF Corse team-mate Miguel Molina and Kobayashi right at the end of the 15-minute Hypercar session.
The Italian’s 2m00.777s was good enough to give Ferrari pole by just three hundredths before the time was scratched out for the infraction on the exit of Les Combes.
Kobayashi moved back to the top of the times after the penalty for the Ferrari was confirmed, his 2m00.812s aboard his GR010 HYBRID LMH giving him a fifth pole of the Hypercar era.
His time was just two hundredths quicker than Molina’s 2m00.836s.
Giovinazzi took third with his previous best of 2m00.973s.
The two Ganassi-run Cadillac Racing entries took fourth and fifth in the hands of Earl Bamber and Sebastien Bourdais.
Bamber’s 2m01.043s in the Ganassi’s full-season V-Series.R LMDh put him within three tenths of the pole, while Bourdais was more than a second slower on 2m02.138s.
Porsche took sixth just a tenth behind the second Caddy with Kevin Estre in the best of the Penske-run factory 963 LMDhs.
His 2m02.306s was six tenths up on the debuting customer 963 run by the Jota team in which Will Stevens got down to 2m02.907s.
Olivier Pla, pole winner for the Spa WEC round last year, was eighth in the solo Glickenhaus-Pipo 007 on 2m02.960s.
Jean-Eric Vergne was the fastest Peugeot driver on a 2m03.217s, while Frederic Makowiecki rounded out the top 10 in the second of the Porsche Penske Motorsport entries with a 2m03.650s.
Gustavo Menezes was 11th in the second Peugeot 9X8 LMH, while Tom Dillmann was 12th in the Vanwall-Gibson Vandervell 680.
The session was red flagged after just a couple of minutes when Brendon Hartley crashed the #8 Toyota at Raidillon straight out of the pits on cold tyres.
Tom Blomqvist took a second LMP2 pole of the season for the #23 United Autosports ORECA-Gibson 07, following up on team-mate Oliver Jarvis qualifying in top spot at Sebring in March.
The Briton posted a 2m05.979s to beat late-improver Louis Deletraz at the top of the times by more than three tenths.
Deletraz’s 2m06.318s in the best of the WRT ORECAs bettered the 2m06.506s from Daniil Kvyat in the fastest of the two Prema entries.
Robin Frijns took fourth in the second WRT car with a time just three hundredths slower than Kvyat.
Ahmad Al Harthy claimed a maiden WEC pole position in GTE Am aboard the ORT by TF Sport Aston Martin.
The Omani driver topped the times before a red-flag stoppage of nearly 10 minutes and improved twice afterwards to claim the top spot by nearly two seconds with a 2m17.216s aboard his Vantage GTE.
Sarah Bovy took a last-gasp second in the Iron Dames Porsche 911 RSR with a 2m19.150s on a lap completed after the chequered flag had fallen.
Luis Perez Companc lost a time good enough for second to a track-limits infraction in his AF Corse Ferrari 488 GTE Evo and ended up fifth.
The stoppage was caused by PJ Hyett when he crashed his Project 1 Porsche at the top of Eau Rouge.
Only 13 of the 14 GTE Am cars took part in the 15-minute session.
The #21 AF Corse Ferrari crashed by Diego Alessi in second free practice on Thursday afternoon was undergoing a rebuild around a fresh shell during the session.
The Spa 6 Hours, round three of the 2023 WEC, begins at 12:45 local time on Saturday.
Hypercar results:
| Cla | # | Drivers | Car | Class | Time | Gap |
|---|---|---|---|---|---|---|
| 1 | 51 |
 Alessandro Pier Guidi  James Calado Antonio Giovinazzi
|
Ferrari 499P | HYPERCAR | 2'00.777 | |
| 2 | 7 |
Mike Conway  Kamui Kobayashi  Jose Maria Lopez
|
Toyota GR010 - Hybrid | HYPERCAR | 2'00.812 | 0.035 |
| 3 | 50 |
Antonio Fuoco  Miguel Molina  Nicklas Nielsen
|
Ferrari 499P | HYPERCAR | 2'00.836 | 0.059 |
| 4 | 2 |
 Earl Bamber Alex Lynn Richard Westbrook
|
Cadillac V-Series.R | HYPERCAR | 2'01.043 | 0.266 |
| 5 | 3 |
 Sébastien Bourdais  Renger van der Zande Jack Aitken
|
Cadillac V-Series.R | HYPERCAR | 2'02.138 | 1.361 |
| 6 | 6 |
Kevin Estre  Andre Lotterer  Laurens Vanthoor
|
Porsche 963 | HYPERCAR | 2'02.306 | 1.529 |
| 7 | 38 |
 Antonio Felix da Costa Will Stevens  Ye Yifei
|
Porsche 963 | HYPERCAR | 2'02.907 | 2.130 |
| 8 | 708 |
Romain Dumas Olivier Pla Franck Mailleux
|
Glickenhaus 007 | HYPERCAR | 2'02.960 | 2.183 |
| 9 | 93 |
Paul di Resta Mikkel Jensen Jean-Eric Vergne
|
Peugeot 9X8 | HYPERCAR | 2'03.217 | 2.440 |
| 10 | 5 |
 Dane Cameron Michael Christensen Frédéric Makowiecki
|
Porsche 963 | HYPERCAR | 2'03.650 | 2.873 |
| 11 | 94 |
Loic Duval Gustavo Menezes  Nico Müller
|
Peugeot 9X8 | HYPERCAR | 2'03.879 | 3.102 |
| 12 | 4 |
Tom Dillmann Esteban Guerrieri  Jacques Villeneuve
|
Vanwall Vandervell 680 | HYPERCAR | 2'04.614 | 3.837 |
| 13 | 8 |
Sébastien Buemi Brendon Hartley Ryo Hirakawa
|
Toyota GR010 - Hybrid | HYPERCAR | ||
| View full results | ||||||
