Vandoorne is Mercedes' reserve driver and was the obvious candidate to replace Hamilton, who was ruled out following a positive coronavirus test.
The Belgian flew out to Bahrain from a Formula E test in Valencia ahead of this weekend's race, but it was later confirmed that Williams agreed a deal with Mercedes to release George Russell.
Posting to social media, Vandoorne admitted he was disappointed about missing out on an F1 return, but respected Mercedes' decision.
“Firstly, I want to wish Lewis Hamilton a speedy recovery and hopefully he'll be back in the car ASAP. Nobody can really replace him,” the Belgian wrote.
“Obviously I'm disappointed not to get the chance to drive for (Mercedes) this weekend.
“After having spent the year travelling to all F1 races and dedicating so much time, physical training, commitment to this programme… it hurts.
“On the other hand, I respect the choice of putting George Russell in the car. He has been one of the standout drivers and he fully deserves this opportunity.
“It's moments like these that make my drive even bigger and I can assure you I'm going to continue giving 100 percent.
“Thank you so much everyone for all your supportive messages. It's been great to see.”
Free Practice 1 for the Sakhir Grand Prix will commence at 0030 AEDT Saturday.
— Stoffel Vandoorne (@svandoorne) December 3, 2020