The Carlin driver led the early stages of the race after a start behind the safety car due to heavy rain at the Belgian circuit. He briefly lost that place to Robin Frijns when the pair pitted together at the end of lap eight, but Magnussen charged past his fellow rookie at Les Combes on their outlap to resume the effective lead of the race.
Later that lap the safety car was deployed after Richie Stanaway had an airborne crash at Les Combes after tagging the back of Carlos Huertas. With the Kiwi having some difficulty getting out of the car, the decision was taken to stop the race.
Although Magnussen was effectively the leader, he was fifth on the road as four cars had not completed their mandatory pitstops before the stoppage.
Of those four, Lewis Williamson and Jake Rosenzweig chose not to pit at all once the race restarted, and both crossed the finish line ahead of Magnussen. However, it was confirmed shortly before the finish that both cars would have 60 seconds added to their race time for not making a pit stop.
That left Magnussen the deserving winner, although Williamson rather cheekily parked his car in the race winner's position in parc ferme. The Scot said afterwards that his team told him not to pit and to treat the remainder of the race after the red flag as a test session.
Nick Yelloly took an impressive second for Comtec, having made his pitstop just as the safety car came out, which enabled him to get between Magnussen and Frijns.
Nico Muller was on the tail of the lead fight throughout the race and came home fourth, while championship leader Sam Bird took fifth to rescue a good amount of points after being put to the back of the grid for running out of fuel in qualifying.
The ISR driver made a few places up in the first couple of laps, and then made an early pitstop to try to get some clear track.
The red flag ruined the chances of that strategy working, but Bird still charged from 15th at the restart to a top five finish to retain his championship lead.
Jules Bianchi was one of the main frontrunners to hit trouble. The Frenchman ran third early on, but lost several places during his pitstop with a problem on the right rear wheel. He was then relegated to the back of the field when his car failed to leave the startline after the red flag.