McLaren's engine partners Honda confirmed the rookie would collect the penalty, that will leave him either last on the grid or starting from the pit lane, after an update aimed at improving reliability.
"Unfortunately Stoffel will receive a grid penalty at his home grand prix, but it is important for us to introduce updates as soon as they are ready," said Honda's Formula One head Yusuke Hasegawa.
Drivers are penalised for exceeding their allocation of power units, and component parts, for the season.
Vandoorne, who will be the first Belgian to compete in his home race since Jerome d'Ambrosio in 2011, has scored one point so far this season with the Honda power unit lacking performance and reliability.
He said he was still looking forward to the weekend and racing in front of his home fans for the first time in Formula One.
"The penalties were kind of inevitable with the issues we had earlier this season. Every new part we bring to the car now is giving us grid penalties and it's a shame to start the weekend like that.
"But with the weather here, there's maybe a lot of opportunities possible."
McLaren announced on Wednesday that the 25-year-old would be continuing with them next season. His Spanish team mate Fernando Alonso, a double world champion, is still considering his options.
Honda said Alonso, who finished sixth in the previous race in Hungary, would not face any grid penalties this weekend.
(Reporting by Alan Baldwin, editing by Jon Boyle)
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