A Honda spokesman said a decision had been made to replace the car's power unit after an issue during Saturday's final practice.
He added that the component in question could have been replaced without a penalty with more time but post-qualifying conditions made that impossible.
Vandoorne has scored one point in 12 races so far this season, and Monza -- the fastest circuit on the calendar -- threatens to be another tough afternoon for a team enduring a power deficit to rivals.
The Belgian's Spanish team mate Fernando Alonso also has a 35 place penalty on a 20 car grid littered with similar mandatory drops imposed as a result of engine and gearbox changes.
The sanctions have become an embarrassment and source of frustration for teams and fans, with calls for the rules to be changed -- although that is easier said than done.
The Red Bull pairing of Max Verstappen and Daniel Ricciardo, who were second and third fastest in Saturday's rain-delayed qualifying, have 20 and 25 place penalties respectively.
Renault's Jolyon Palmer and Nico Hulkenberg took 15 and 10 place drops while Toro Rosso's Carlos Sainz also took a 10 place hit.
Haas's Romain Grosjean, who was already last on the grid after crashing in the first phase of qualifying, will also have a meaningless penalty for a gearbox change.
Taking into account all the other penalties, Honda reckoned Vandoorne should start in 18th place.
Triple world champion Lewis Hamilton starts on pole position, his record 69th, with Canadian 18-year-old rookie Lance Stroll alongside on the front row for Williams.
Ferrari's championship leader Sebastian Vettel starts his team's home race in sixth place.
(Reporting by Alan Baldwin, editing by Pritha Sarkar)
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