The governing body initially said no points would be given out after the incident-strewn race on a damp track saw the safety car run for much of its 12 laps and finished under caution.
Caio Collet took victory for Van Amersfoort Racing, with Taylor Barnard second for Jenzer Motorsport in his maiden series podium and Prema driver Paul Aron in third.
The series said in a press release after the race: "As the minimum of two racing laps were not completed without the intervention of the Safety Car, no points are awarded for the race as per the Sporting Regulations."
But the governing body backtracked several hours later, deciding to award full points.
It said the two-lap rule didn't apply because the race ran to full distance, having been shortened from 15 to 12 laps on Thursday in a pre-event race director's note due to concerns over tyre safety.
The U-turn has an impact on the championship fight, with Aron boosted to joint second with Campos driver Pepe Marti on 102 points.
Standings leader Gabriel Bortoleto, who failed to finish Saturday's race after contact with Dino Beganovic (Prema) holds the lead on 144 points.
Marti also failed to finish after coming together with Gabriele Mini (Hitech) in the fight for 10th at Pouhon, 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 of their races in an incident which was investigated by the stewards - with no further action taken on Marti.
Zak O'Sullivan, who finished the race fourth from Prema, was dropped out the points by a five-second post-race penalty.
He was found to have gone off-track and gained an advantage in his battle with poleman Hugh Barter (Campos) at Turns 3 and 4.
The FIA stewards said: "Having considered the matter extensively, the Stewards determined that Car 3 entered Turn 3 behind Car 25.
"Both cars misjudged their exit speed at Turn 3 and subsequently went off track at Turn 4.
"However, Car 3 was carrying more speed, off track, and as such was able to overtake Car 25 easily at the exit of Turn 4.
"The excess speed and advantage were verified by the driver of Car 3 and via race telemetry.
"Car 3 did not give back the position and thereby gained a lasting advantage."
The points being awarded benefit his team-mate Aron, dropping the Briton to fourth in the standings.
