Team principal Fred Vasseur said: “We had an issue with the fuel system when we fuelled the car one hour before, and it was too late to change something.
“It's a shame because he was in good momentum after Monza, Singapore, and so on, but it is what it is.”
Sainz had been due to start from 12th on the grid following a poor qualifying session on Friday evening.
The 29-year-old redeemed himself in part by qualifying fifth for the sprint shootout, and finishing sixth at the chequered flag of the 19-lap race.
It is only the second time in his F1 career, now in its ninth season and after 178 grands prix, that Sainz has failed to start a race.
The other occasion was ahead of the 2020 Belgian Grand Prix, whilst driving for McLaren, due to his car sustaining a power unit issue.
It leaves the second half of the grid in unusual shape as Sergio Perez was due to line up 13th but will now start from the pitlane after Red Bull opted to change his power unit following a heavy crash during the sprint.