The incident caused a late red flag in the session, which delayed Q2, as marshals worked to clear Antonelli's stricken car.
Qualifying got underway again pretty soon, with the young Italian's crash only causing a five-minute delay to proceedings.
However, it will be gutting for Antonelli, who will now start down in 15th in the race, at a track that is incredibly difficult to overtake around.
Antonelli suffers after great start
It is the second race weekend in a row that Antonelli has not made it through to Q3, with the Mercedes driver also suffering at his home race in Imola last time out.
The 18-year-old Italian is finally showing signs of the rookie that he is, after an incredible start to the season.
He is currently sat in seventh in the drivers' championship, with 48 points from the opening seven race weekends of his career in the sport.
It continues a miserable weekend for Mercedes, who seemingly have a lack of pace around the principality, not being able to match Red Bull, Ferrari and McLaren throughout the weekend.
After Antonelli's incident, his Mercedes team-mate George Russell also was eliminated from qualifying, after losing power while in the tunnel section of the track, prompting another red flag and a second delay to qualifying.
Q2 got back underway at 16:44 local time, but both Mercedes cars were missing from the track.