An incident-strewn race on a damp track, which was shortened by three laps due to continuing concerns over tyre safety, saw the safety car run for much of its 12 laps.
Collet, who lined up fourth for Van Amersfoort Racing, took third out of Turn 1 before moving into second before the Kemmel Straight.
He then took the lead from Taylor Barnard (Jenzer) at Blanchimont before the first safety car was deployed.
Enduring two restarts, the race then finished under the safety car as dark clouds threatened rainfall.
It was Collet’s first F3 win since Zandvoort last year, with Barnard securing second for his maiden F3 podium ahead of Prema driver Paul Aron.
With the track still damp from Saturday’s heavy rainfall and with more rain set to fall, poleman Hugh Barter (Campos) led off the line.
Barnard took second from Aron at Turn 1 before the Estonian and Collet fought for third, with Collet emerging ahead.
Barnard then moved into the lead on the Kemmel Straight, with Collet in second ahead of Barter before the Brazilian took the lead at Blanchimont.
The first safety car was then deployed after Sebastian Montoya (Hitech) was tagged by VAR driver Rafael Villagomez, the former stopping on track after Turn 8.
Racing resumed on lap four, with Zak O’Sullivan (Prema) passing team-mate Dino Beganovic for fifth.
But action was again suspended soon after as Gabriele Mini (Hitech) and Campos driver Pepe Marti came together in the fight for 10th, the Alpine Academy member tagging the Spaniard and sending him into a spin, with Mini’s race ending.
Marti then attempted to rejoin but crashed into the side of Rodin Carlin driver Ido Cohen, ending both drivers’ races in an incident which will be investigated after the race.
The safety car ended on lap eight with O’Sullivan taking fourth from Jonny Edgar (MP Motorsport) as he locked up at Turn 1, with team-mate Franco Colapinto attempting to repeat the move but staying behind.
Further back, championship leader Gabriel Bortoleto (Trident), who started 15th, made it past Beganovic for ninth, but suffered contact from the Prema rookie.
Bortoleto slowed before coming to a stop on track having suffered a puncture, prompting yet another safety car.
This led the field across the line as the chequered flag waved, with Collet taking victory from Barnard and Aron.
Title contender O’Sullivan finished fourth, with Edgar fifth and Colapinto sixth. Poleman Barter was seventh ahead of Nikola Tsolov (ART Grand Prix), with Beganovic and Hitech driver Luke Browning rounding off the top 10.
F3 Spa: Race 1 Result (12 laps):
| 1 |  C. Collet Caio Collet Van Amersfoort Racing |
17 | 12 | – | 10 | 1 | |||||
| 2 |
T. Barnard Taylor Barnard Jenzer Motorsport |
27 | 12 | +0.500 | 0.500 | 9 | |||||
| 3 |
P. Aron Paul Aron Prema Powerteam |
1 | 12 | +0.900 | 0.400 | 8 | |||||
| 4 |  Z. O’Sullivan Zak O’Sullivan Prema Powerteam |
3 | 12 | +1.300 | 0.400 | 7 | |||||
| 5 | J. Edgar Jonny Edgar MP Motorsport |
12 | 12 | +1.500 | 0.200 | 6 | |||||
| 6 |  F. Colapinto Franco Colapinto MP Motorsport |
10 | 12 | +1.600 | 0.100 | 5 | |||||
| 7 |
H. Barter Hugh Barter Campos Racing |
25 | 12 | +2.200 | 0.600 | 4 | |||||
| 8 |
N. Tsolov Nikola Tsolov ART Grand Prix |
9 | 12 | +2.500 | 0.300 | 3 | |||||
| 9 |
D. Beganovic Dino Beganovic Prema Powerteam |
2 | 12 | +3.200 | 0.700 | 2 | |||||
| 10 |
L. Browning Luke Browning Hitech Pulse-Eight |
16 | 12 | +3.300 | 0.100 | 1 | |||||
| 11 |
L. Fornaroli Leonardo Fornaroli Trident |
4 | 12 | +3.500 | 0.200 | ||||||
| 12 |  G. Saucy Gregoire Saucy ART Grand Prix |
8 | 12 | +4.400 | 0.900 | ||||||
| 13 |
N. Bedrin Nikita Bedrin Jenzer Motorsport |
26 | 12 | +4.700 | 0.300 | ||||||
| 14 |  S. Flörsch Sophia Flörsch PHM Racing by Charouz |
29 | 12 | +5.300 | 0.600 | ||||||
| 15 |  K. Frederick Kaylen Frederick ART Grand Prix |
7 | 12 | +5.600 | 0.300 | ||||||
| 16 |
F. Simonazzi Francesco Simonazzi Rodin Carlin |
21 | 12 | +6.200 | 0.600 | ||||||
| 17 |
M. Boya Mari Boya MP Motorsport |
11 | 12 | +6.500 | 0.300 | ||||||
| 18 |
R. Faria Roberto Faria PHM Racing by Charouz |
30 | 12 | +7.600 | 1.100 | ||||||
| 19 | A. Garcia Alex Garcia Jenzer Motorsport | 28 | 12 | +10.300 | 2.700 | ||||||
| 20 |
T. Smith Tommy Smith Van Amersfoort Racing |
19 | 12 | +10.800 | 0.500 | 1 | |||||
| 21 |
C. Mansell Christian Mansell Campos Racing |
24 | 12 | +11.800 | 1.000 | 1 | |||||
| 22 |
O. Gray Oliver Gray Rodin Carlin |
20 | 12 | +12.600 | 0.800 | 1 | |||||
| 23 |
M. Shin Michael Shin PHM Racing by Charouz |
31 | 12 | +13.100 | 0.500 | ||||||
| 24 |  R. Villagomez Rafael Villagomez Van Amersfoort Racing |
18 | 12 | +18.800 | 5.700 | ||||||
| dnf |
G. Bortoleto Gabriel Bortoleto Trident |
5 | 8 | 4 laps | Retirement | ||||||
| dnf |
G. Minì Gabriele Minì Hitech Pulse-Eight |
15 | 3 | 9 laps | Retirement | ||||||
| dnf |
P. Martí Pepe Martí Campos Racing |
23 | 3 | 9 laps | Retirement | ||||||
| dnf |
O. Goethe Oliver Goethe Trident |
6 | 3 | 9 laps | Retirement | ||||||
| dnf |  I. Cohen Ido Cohen Rodin Carlin |
22 | 3 | 9 laps | Retirement | ||||||
| dnf |  S. Montoya Sebastian Montoya Hitech Pulse-Eight |
14 | 11 | Retirement |