Exclusion from qualifying is the standard outcome for the offence, with Alex Albon the last driver to get such a penalty at last year’s Australian GP.
Bottas stopped on track in Q1, reporting no power, having already done enough to progress through to Q2 in 11th place.
He was not able to take part in the second session, and thus without setting a time he was classified 15th after it.
However, following the session the FIA discovered that there was insufficient fuel in the car to fulfil the mandatory requirement of one litre left in the car for testing.
When a car stops on track in qualifying the FIA also calculates how much fuel would have been used to get back to the pits because cars are obliged to return under their own power, which is not the case at the end of races.
The FIA’s technical delegate Jo Bauer noted: “After the qualifying session today it was checked on car number 77, that a 1-litre fuel sample plus the amount of fuel that would have been consumed to drive back to the pits could be taken (technical regulations article 6.5.2). It was possible to take a 0.090 litre sample.
“As the amount of fuel needed to produce a 1-litre sample plus to return the car to the garage was calculated as 2.39 litre, I am referring this matter to the stewards for their consideration.”
The stewards noted that there were no mitigating circumstances for Alfa Romeo having not been able to provide a sufficient fuel sample.
With the Alfa driver’s exclusion confirmed, he can start from the back of the grid. This means Sergio Perez, Yuki Tsunoda, Zhou Guanyu, Nyck de Vries and Kevin Magnussen have each gained a place.
Asked by Autosport about the issue in qualifying, Bottas said he didn’t know why the car had stopped.
"Not yet,” he noted. “We need to find out. There's obviously many reasons that can cause the engine to stop. So I don't know. It's a shame, but not much I can do for that.
"I didn't actually see the final time from Q2 I don't know how far I was from the from the cut-off, but at least we made it through to Q2 this time, and it's actually extremely close.
"So I think we made some steps from yesterday. So now we still need to wait till tomorrow that we see how is the pace."
Bottas said the latest upgrade package has improved the car: "It's a step. I definitely feel the step and I think today we managed to extract a bit more with a setup. It seems like it needed a different set-up in terms of ride height and everything.
“So now it actually felt a step, more high-speed load basically, without affecting the low-speed performance.”