The team broke curfew -- during which members associated with the operation of the car must leave the track -- after the engine the double world champion used on the opening day of practice suffered a hydraulic issue.
Rules restrict drivers to no more than four power units and its constituent components for the duration a season, and Alonso has long exceeded his allocation as McLaren continues to struggle with a lack of reliability from their Honda engines.
Sunday's grand prix at Suzuka is the home race for the Japanese manufacturer, who will part ways with McLaren at the end of the season after three years of dismal performances, with the Surrey-based team switching to Renault power units.
Honda will instead supply engines to Red Bull's junior team Toro Rosso, currently powered by Renault, whose Spanish driver Carlos Sainz has also been hit with a 20-place penalty for exceeding his allocation of engine components.
Ferrari's Kimi Raikkonen and Valtteri Bottas of Mercedes were also handed grid penalties, with both Finns dropping five places for unscheduled gearbox changes.
The Italian team was forced to replace Raikkonen's gearbox, which has to be used for at least six straight races, after the 2007 champion damaged it in a crash during Saturday's final practice session.
Briton Jolyon Palmer will also drop 20 places for exceeding his allocation of power unit components after his Renault squad fitted his car with a new turbo charger, MGU-H and internal combustion engine.
(Reporting by Abhishek Takle in Suzuka; Editing by John O'Brien)
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