The third and final phase of the session was red-flagged with two minutes and 26 seconds remaining when Perez smashed into the barriers at the tunnel exit, the fastest point of the street circuit.
The 21-year-old was attended to by the emergency medical team in his wrecked Sauber, while marshals shielded the scene with a large sheet.
He was then extracted and taken away in an ambulance while the shattered car, with most of its side missing and wheels dangling, was lifted and taken back to the pits on a truck.
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Perez escaped serious injury but his concussion means he will be unable to race in the Monte Carlo event.
The Mexican rookie also suffered a sprained thigh but no broken bones. Perez will stay in the Prince Grace hospital at least overnight.
"Of course we are very relieved that Sergio wasn't seriously injured," said team boss Peter Sauber.
"Up to the accident he was doing very well in qualifying, and also better than expected as he had outperformed all his direct competitors."
Technical director James Key added: "First and foremost we are obviously relieved with the reports that Sergio is okay. It's always very worrying for a team when you see an accident of that magnitude, so it's good to hear that he is fundamentally okay.
"We are looking into what happened. There is no indication at the moment from the data we have seen that there was a problem with the car. But we have to talk to Sergio to investigate further what happened."
"The most important thing was to hear that Sergio is okay," said championship leader Sebastian Vettel, who took pole.
"There was a bit of a shadow over qualifying when you see a colleague crash and not jumping out of the car immediately," he added. "It is difficult to keep the focus and you don't feel 100 percent well when you don't know what is going on."
Jenson Button, who had a similar accident at the same spot in final practice with BAR Honda in 2003 and had to miss the showcase race that year, sympathised.
"I know how much it hurts (to crash there)," he said.
The rookie's absence means team-mate Kamui Kobayashi will be the only Sauber in the race.
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