The Dane, who is leaving the US-owned team at the end of the season, was given a 10-second penalty and two points for causing a collision with Alpine's Pierre Gasly at Monza on Sunday.
The rules state that any driver reaching 12 points in a 12-month period be suspended. The last Formula 1 driver to receive a ban of any sort was Frenchman Romain Grosjean, for dangerous driving in 2012.
Stewards said in a statement that Magnussen's super licence had been suspended for his next race, after which the points will be removed.
Round 17 of the 24-race championship is in Baku on September 15th.
Ferrari reserve Oliver Bearman, who will be racing for Haas next season, could be in line to replace him after making his debut in Saudi Arabia in March as a stand-in for Carlos Sainz at Ferrari, finishing seventh.
"I don’t know what’s happening with these penalties. What’s the point?" Magnussen fumed.
"We had a slight contact into turn four, no damage on either car, no consequence, nobody lost anything. We both missed the corner but we’re racing. I just don’t get the point honestly."
Gasly told reporters he would be happy to argue on Magnussen's behalf.
"Someone told me he got a 10-second penalty. I'm a bit surprised for that because he tried, but it was a bit of wheel-to-wheel and in the end, I really didn't lose any time," said the Frenchman.
"I hope somehow they can revert on that because that (a ban) would be definitely unfair."
