The Red Bull driver secured pole position during a frenetic qualifying session at the Red Bull Ring, which was overshadowed by a spate of track limit penalties.
But nearly two hours after the chequered flag, the FIA stewards announced that Verstappen was under investigation for an incident with Magnussen.
According to a short statement issued by the FIA, Verstappen is alleged to have held up Magnussen at Turn 1 during the first segment of qualifying.
Magnussen said that the incident with Verstappen happened at the start of his final run in Q1.
Onboard footage showed that Verstappen was driving slowly on the exit of Turn 1 while Magnussen was beginning his hot lap.
Although he lost time as he had to manoeuvre his way around the Red Bull, Magnussen's lap was later deleted anyway for a track limits infringement.
Speaking after the session, as he ended up 19th, Magnussen said: "It's all so tight at the moment. I had traffic with Verstappen at Turn 1 on the first lap of my final run, but that lap was deleted for track limits – it wouldn't have counted anyway.
"Then on my second attempt, I had a downshift fault, it wouldn't downshift, so it cost me a little bit of time at Turn 3 as I was in the wrong gear.
"When it's this tight, in fact, it's unbelievably tight – a little issue like that is very costly. Normally you can get away with something like this, but we were just on the wrong end of it today."
Verstappen risks a grid penalty if the stewards find him to be guilty of impeding, and the fact that Magnussen's lap was deleted will likely make little difference to the stewards' decision on whether or not to take action.
If Verstappen does get dropped down the order, then that would hand pole position for the Austrian GP to Ferrari's Charles Leclerc, who ended qualifying in second spot ahead of his team-mate Carlos Sainz.
