Stannard, 26, has been out with a back injury since April and will not recover in time for the Tour, which starts in Yorkshire on July 5.
The time trialist and general domestique came off his bike during the Gent-Wevelgem last month, suffering a fractured vertebra, but had hoped to return in time for the biggest of the Grand Tours.
But he will miss the showpiece event after consulting a specialist.
"In the week after the crash I visited a neurosurgeon and had CT and MR scans," Stannard said on the Team Sky website.
"When the results from those came through [team doctor] Phil Riley booked me an appointment with a pure spine specialist in London and he was the one who detailed the extent of my injuries.
"He said I’d been really lucky not to suffer any permanent damage because my vertebrae had been quite badly damaged."
Stannard admitted his disappointment at the blow, but indicated he is still hoping to return to action this season.
"I’ve got to have another X-ray at the 12-week mark to check everything is healing okay and they can guarantee I won’t be putting myself at risk by riding again.
"We’re confident I’ll be riding again before the end of the season though, so that’s what I’m focusing on. I’m eager to get back in the saddle but it’s in the hands of the experts."
- Sports & Recreation