Kubica had a fastest lap of 1 minute, 19.191 seconds at the 2.6-mile Interlagos track, 0.309 in front of Vettel and 0.345 ahead of Hamilton.
Felipe Massa was fourth, 0.544 behind Kubica, and Alonso fifth with a time 0.600 slower than Kubica's.
It was the last practice before qualifying later Saturday.
Five drivers are still in contention for the Formula One title with two races to go, but only Alonso can clinch the championship in Brazil.
Webber, Hamilton, Vettel and Jenson Button are trying to extend the title race into the Nov. 14 season finale in Abu Dhabi.
Webber, trailing Alonso by only 11 points, ran only six laps, the fewest among the title contenders in the one-hour practice under light rain. His time was more than a second slower than Kubica's.
Button was ninth with his McLaren, 0.973 behind the fastest time.
It rained overnight and all morning in Sao Paulo. The rain stopped at times during the session, but it was not enough to dry the track. It improved significantly toward the end of the practice, allowing for quicker times.
Hamilton went wide exiting a corner at the end of the back straight but was able to keep racing. Bruno Senna of Hispania and Jaime Alguersuari of Toro Rosso also had close calls under slippery conditions but were able to stay on the track without losing control.
The Red Bull drivers set the pace in the first day of practices on Friday, with Vettel leading Webber in both sessions in dry conditions. Their rivals had been hoping for rain on Saturday to try to reduce Red Bull's advantage and even the field going into qualifying and the race on Sunday.
Red Bull has won the pole 14 times in 17 races so far, nine with Vettel and five with Webber. The team has not been able to translate that dominance into the races, however, because of driver mistakes and mechanical failures. Vettel has won only three times this season and Webber four.
Rain caused havoc in last year's qualifying session at Interlagos, sending top contenders to the back of the grid. Button had to start in 14th place, with Vettel in 15th and Hamilton in 17th.
To win his third F1 title in Brazil, Alonso needs to win Sunday's race and hope Webber finishes fifth or worse. The Spaniard also can secure the title if he finishes second and Webber places eighth or worse, Hamilton is fourth or worse and Vettel second or worse.
The drivers' championship has been decided at the Brazilian GP in the past five years. Button won it with Brawn GP in 2009, as did Hamilton with McLaren in 2008 and Kimi Raikkonen with Ferrari in 2007.
Alonso won his first two titles at Interlagos in 2005 and '06 with Renault. He is debuting with Ferrari after a disappointing year with McLaren in 2007 and two seasons with Renault, before replacing Kimi Raikkonen in the Italian team.