The Japanese firm have provided neither a competitive or reliable power unit in 2017, and the new MGU-H and turbo chargers in Alonso and Vandoorne's cars are their sixth of each component this year, triggering automatic 15-place grid penalties for both drivers.
While Alonso will also run a new Internal Combustion Engine, it is his fourth and therefore does not incur a penalty.
This year the FIA clamped down on a loophole in the rules that allowed teams to stockpile components and take a big penalty at a single event in order to avoid penalties at future events. "This is to prevent the stockpiling of spare power unit elements".
With a 30 place grid penalty, Stoffel Vandoorne's debut season isn't going to get easier anytime soon.
Alonso - who retired from FP2 with a gearbox failure - isn't due to run the upgrade for the remainder of the weekend however, with Honda keen to study the data collected on Friday before a likely debut at the Austrian GP in a fortnight, which is likely to include further updates to the hybrid system.
"We have some penalties already to start the weekend, which is not ideal but this is the situation we are in", Vandoorne said. "I think his value has never been higher, with what he's done at the Indy 500, and with what he's done sometimes with that McLaren". "We will try and make our best focus maybe a bit more on race runs and hopefully we can play a little bit during the race".
"As I said many times, I want to win next year and I don't want to gamble too much in any decision, I want to be more or less safe in wherever I go for", he said.
Not just that, changing the engines will leave both Alonso and his teammate dead last on the grid.
Securing and announcing a Mercedes supply for 2018, could amount to the same thing in Alonso's mind, and convince him to stay on for 2018.