Adding to what has already been a troubled weekend for the French manufacturer, with Pierre Gasly starting 19th for both the sprint and main race following mechanical problems and a crash on Friday, the squad was hit by further woes on Saturday.
Ocon had qualified 13th for the sprint, one spot behind where he will line up for the race, but he will now no longer take up his place on the grid.
Alpine confirmed after the sprint shootout qualifying session that Ocon's car was being removed from parc ferme.
With the sprint format meaning that drivers are locked into settings from the start of Friday qualifying, changes that Alpine has planned for his car mean he will face a punishment.
The new regulations have laid out that any change in car parameters between the start of qualifying and the beginning of the sprint race means he will start both Saturday's short race and the main grand prix on Sunday from the pitlane.
Alpine's difficult weekend has come after it held out high hopes of a good performance lift from a revised floor.
While there was always the risk of it facing trouble from introducing major new components during the compressed sprint race timetable, team principal Otmar Szafnauer said it was ultimately reliability niggles that had cost it the most.
Speaking to Motorsport.com earlier in the weekend, Szafnauer said: "We made that choice. Maybe it's bitten us, but we couldn't have predicted reliability issues. Had we known that we had a half hour of FP1, we would have made a different choice.
"So, hindsight is a lovely thing here. But with an hour, we thought we had enough time to make the requisite set-up changes."
Gasly had been held back on Friday by a car fire that was triggered by a hydraulic leak, and then he hit the barriers early in Q1 to put himself out of action.
