The team found damage to the unit, and was forced to replace it before the required six consecutive events for a gearbox had been completed.
That meant the gearbox should have lasted until the Japanese Grand Prix, when the next penalty free change would have been permitted.
Hulkenberg had earlier finished ninth in the opening practice session, ahead of team-mate Jolyon Palmer and seventh in the second session on Friday, behind only the Red Bull's, Ferrari's and Mercedes drivers.
Penalty-free gearbox changes
In the technical delegate's report, it was also revealed that Romain Grosjean will take a new gearbox, seeing as he had reached the required six events on a single unit, while both Fernando Alonso and Carlos Sainz are able to take a new unit, as they both retired from the British Grand Prix.
Hulkenberg's team-mate Palmer will also take a fresh gearbox, as he did not start the last race, and is "in conformity with Article 23.5a of the 2017 Formula One Sporting Regulations."
Both Valtteri Bottas and Daniel Ricciardo were forced into using a spare gearbox at the last event, and under the rules, technical delegate, Jo Bauer, issued the notice saying: "Therefore they may use a new gearbox at the Event and the six consecutive Event will start here in accordance with Article 23.5.a."
Spate of gearbox penalties
The news of Hulkenberg's penalty is the fourth such like penalty, in the last three races.
In Austria, Lewis Hamilton was handed a five-place penalty as Mercedes were forced to change his gearbox, while at Silverstone, both Hamilton's team-mate Bottas and Ricciardo were handed their own five-place grid drops.