The three-time Olympian, who had finished 15th and eighth in her previous appearances, had looked set to line up in the final six after semi-final race leader, American Lindsey Jacobellis, dramatically fell.
But that error also meant Gillings had to alter her line, losing speed that ultimately meant she crossed the finish just half a metre behind Italy's Michela Moioli, who claimed the last qualifying spot.
She went on to finish fourth in the B final to rank ninth overall while Eva Samkova took gold for the Czech Republic.
"I'm really disappointed about the photo finish and not quite making the final but it can be pretty small margins in this sport. One of the officials said I'd made it but it flashed up on the screen about 15 seconds later that I hadn't," she said.
"Lindsey (Jacobellis) fell in front of me and I had to change my line a little bit and that cost me some speed and is why I got caught on the line.
"My aim coming into the competition was to ride as well as I could and stay on my feet."
Gillings, 28, has overcome countless injuries including crushing her foot, which left the bones inside looking like cornflakes, in 2005.
Doctors said she'd never snowboard competitively again but she's already looking towards a fourth Olympic campaign in Pyeongchang.
"This is my first Olympics where I've not had an injury," she added.
"I'll keep going as long as I can do, I still love the sport and there is no reason to stop unless something really makes me.
"Age wise I'm fine, the last few Games there have been medallists in the early 30s and I'll only be 32 at the next Games.
"Experience plays a big role in snowboardcross, so as long as the funding is there and I'm still enjoying it, there is no reason not to go for another one."
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