The Dane crashed at the exit of the 180mph Eau Rouge/Raidillon corner, bringing the race to a halt because of extensive damage to the barriers.
He was taken to hospital with a left ankle injury.
Magnussen, 23, later wrote on Twitter: "On my way home now with a sore ankle but will be ready for Monza."
Renault driver Kevin Magnussen says he will be fit for next weekend's Italian Grand Prix despite a huge crash in Belgium on Sunday.