The four-time champion clocked one minute 11.622 seconds, 0.025 faster than the 20-year-old Mercedes driver who had topped the second practice at the Interlagos circuit on Friday.
Verstappen is set to start Sunday's race from the back of the grid after collecting a penalty for an engine change, while Ferrari's Lewis Hamilton and Charles Leclerc also face grid drops for taking new internal combustion engines.
McLaren's Lando Norris, fastest in FP1, was third quickest on Saturday, 0.131 off the pace, with Mercedes' George Russell fourth. Russell will take a five-place grid penalty, also for an engine change.
Leclerc was fifth fastest, while teammate Hamilton finished 12th after an apparent engine issue. The 41-year-old Briton reported "strange" engine vibrations and smoke in the cockpit over the radio before stopping.
Aston Martin's Lance Stroll completed only seven laps due to a suspected energy recovery system issue, finishing last.
Brazilian Rafael Camara, making his season debut after replacing Esteban Ocon at Haas, finished the session 15th, ahead of his teammate Oliver Bearman. Audi's Gabriel Bortoleto, the other local driver, was 10th fastest.
Qualifying takes place later on Saturday (19.00 CET), with rain expected but yet to arrive at the atmospheric Brazilian circuit.