The Mercedes driver completed just four timed laps and ended up fifth overall, with team mate Nico Rosberg leading the timesheets.
Rosberg lapped more than a second faster than anyone else, the German's best time of one minute 53.989 seconds comparing to the next quickest of 1:55.224 set by Russian Daniil Kvyat for Red Bull.
Red Bull's Australian Daniel Ricciardo was third and Toro Rosso's Carlos Sainz fourth on a rain-soaked track with more wet weather expected in the afternoon and much heavier thunderstorms over the weekend.
Parts of Texas are on flood alert with talk of possible extreme rainfall in the Austin area on Saturday when qualifying takes place.
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Further south, Mexico, which hosts the next round of the championship next weekend, is braced for the arrival of one of the most powerful storms in history with Hurricane Patricia heading towards the Pacific Coast.
Hamilton needs to beat Ferrari's Sebastian Vettel, who has a 10 place grid penalty for Sunday's race due to an engine change, by nine points and Rosberg by two to retain his title and become a triple champion.
A Mercedes one-two, with Hamilton first, would do the trick and the Briton has a great record in Austin with two wins in the last three races there.
Friday's session started wet, although conditions were changeable, but there were few incidents despite a couple of spins.
Finland's Valtteri Bottas gave his pit crew a scare, forcing some mechanics to jump out of the way when he came in and skidded to a halt.
"Sorry for that," he said over the radio as he departed again.
Vettel was sixth fastest, with Toro Rosso's Max Verstappen seventh and Ferrari's Kimi Raikkonen eighth.
Manor Marussia's Alexander Rossi, who will be the first American to compete in a U.S. Grand Prix since 2007, was 18th of the 20 drivers.
(Editing by Tony Jimenez)
