The Virtuosi Racing driver went third quickest in qualifying on Friday, setting his fastest lap after the third red flag in a disjointed session.
But the FIA found his team could not supply the required 0.8kg of fuel from his car in parc ferme after qualifying, in breach of the technical regulations.
This meant the Australian was stripped of all his times, dropping him to the back of the grid for both races.
Marcus Armstrong will now start from P3 in the feature race, with Dennis Hauger taking pole in the sprint for Prema Racing, as drivers who qualified behind Doohan move up a place on the grid.
In their report, the FIA said the team admitted to miscalculating the fuel load during the “unusual” session and said there was “no intent of wrong-doing involved.”
The FIA said: “The Stewards acknowledge the Team Manager's statement that this was an unusual session in terms of the number of red flags that were issued. On their part, the Team affirmed that they miscalculated the fuel load.
“Having considered the matter extensively, the Stewards conclude that there is no intent of wrong-doing involved. However, there is no dispute that the Technical Regulations have been breached and the standard penalty for such a breach is, therefore, assessed.”
The first of the session’s three red flags came after Theo Pourchaire’s ART Grand Prix-run car caught fire. Smoke had been plummeting from the rear around the previous lap, before he stopped at the side of the track and the fire became visible. It came after he ended up in the wall at Turn 24 during practice, prompting a red flag and ending his session prematurely.
The second came after Carlin’s Logan Sargeant hit the wall on the exit of Turn 17, returning the field to the pitlane.
There was a third red flag with five minutes remaining, but it appeared to be caused by a GPS alarm rather than an on track incident.
Several other drivers were handed grid penalties for various infringements during qualifying.
Juri Vips, who was set to start P3 for Saturday's sprint, will drop three grid places for impeding Enzo Fittipaldi during the session, and receives one penalty point on his record, while Frederik Vesti was handed a three-place penalty and one point on his record for impeding Boschung.
Olli Caldwell will drop three grid places for impeding Vips at Turn 22, with another penalty point bringing his total so far for the season to eight. 12 points during the season results in a race ban.
Clement Novalak drops five places and has three points added to his record for impeding Caldwell during the session. Novalak was approaching Turn 22 when Caldwell approached on a flying lap and was forced to jerk to the left to avoid a collision having not checked his mirrors as he moved across the track.
Amaury Cordeel will drop 10 places and was handed four penalty points for not heeding the warning flags after Sargeant’s accident.
Doohan's qualifying disqualification was similar to that which saw Sebastian Vettel disqualified from last season’s Hungarian Grand Prix, losing the Aston Martin driver second place.
