The 37-year-old Australian made the most of a brief lull in the rain towards the end of the session to lap the shining, anti-clockwise Interlagos circuit with a best time of one minute 27.891 seconds in his Red Bull.
Team mate and quadruple champion Sebastian Vettel, who is aiming for a record-equalling ninth win in a row and 13th of the season in Sunday's season-ender, was 17th on a morning when times were meaningless.
Most drivers opted to save tyres for later qualifying, with the rain threatening to last well into the afternoon.
"Everybody's sitting in the garage trying to save their extreme tyres because we haven't got that many of them," Red Bull principal Christian Horner told BBC television during the session.
Frenchman Romain Grosjean was second quickest with Lotus team mate Heikki Kovalainen, standing in for the absent Kimi Raikkonen, third and fellow Finn Valtteri Bottas fourth for Williams.
Germany's Nico Rosberg, who was fastest in both Friday practice sessions, did not set a timed lap for Mercedes while British team mate Lewis Hamilton was 11th on team principal Ross Brawn's 59th birthday.
Webber, twice a winner in Brazil, is leaving Formula One after Sunday's race to start a new life with Porsche in endurance racing.
(Writing by Alan Baldwin in London, editing by Clare Fallon)
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