The Pole's Citroen DS3 RRC was hit by a repeat of the hydraulic issue that slowed him through the morning.
The problem returned on the first stage out of service on Saturday afternoon and he retired just 700 metres into Loule 2, the day's final test.
The team cannot confirm the precise nature of the failure until the WRC2 machine returns to Faro, but the suspicion is that it is related to the hydraulic problems on the car.
Talking about the problem after SS9, Kubica said: "The gearbox failed and I had to drive the rest of the stage with one hand.
"Given that I drove like this, I think I did a good job."
A decision on whether Kubica returns for the final day will be taken during the evening, but he will be keen to tackle the longest stage of the rally, the 34-miler through Almodovar, after commenting how much he enjoyed driving that test on the recce.