Sebastien Buemi, Ryo Hirakawa and Brendon Hartley had recovered from two separate time penalties to extend its championship lead over the Le Mans 24 Hours-winning #51 Ferrari 499P Le Mans Hypercar on its home turf.
But a bulletin issued by the stewards hours after the race stated that the GR010 HYBRID LMH had exceeded "the maximum released powertrain power" stipulated by the Balance of Performance, which is governed by the technical regulations.
The offence, which occurred on lap 190 of 200, was the car's second infringement of the race after it received a reprimand for the same issue on lap seven.
The second infringement came two laps before Hartley took fourth from the #5 factory Porsche 963 LMDh of Frederic Makowiecki into Turn 1.
Because the penalty was issued after the race, the stewards stipulated that a five-second stop-go penalty would be converted to a 50-second post-race penalty, which pushes the Toyota behind the #5 Porsche and #51 Ferrari.
This had also finished ahead of the Porsche on the road until it too was hit with a 45-second post-race penalty for James Calado overtaking Makowiecki off the track on the pit straight.
Rather than extending its championship lead from 25 to 29 points with two rounds to go, the #8 car's advantage is now reduced to 23 points.
Buemi was handed a 10s penalty at his first pitstop for nudging Antonio Giovinazzi's #51 Ferrari at the first corner of the race, before being slapped with a one-minute stop-go for contact with Satoshi Hoshino's d'Station Aston Martin Vantage GTE on the run to Ascari that sent the Japanese into the barriers.
The sister #7 Toyota of Mike Conway, Jose Maria Lopez and Kamui Kobayashi took its third victory of the season at Monza after defeating the #50 Ferrari driven by Miguel Molina, Nicklas Nielsen and Antonio Fuoco.
