Sebastian Vettel and Kimi Raikkonen then set the pace on their Ferraris, but both face difficult races as engine changes will see them each get 10 grid-place penalties.
IndyCar has put a 10-place penalty on him for engine violations from the Indianapolis 500.
Hamilton was handed a five-place penalty following a gearbox change, and then an engine failure shunted him to he back of the grid.
Misery ensued, with the Briton handed a five-place penalty following a gearbox change before an engine failure in qualifying sent him to the back of the grid.
Charles Pic will start from the back of the grid after receiving a 10-place penalty for exceeding the number of engines allowed during the season.
If Hamilton does receive reprimand he will be hit with a 10-place penalty for the next race in Monaco – the worst race on the schedule for overtaking.
Sauber's Mexican Sergio Perez was given a three-place drop for the same offence as Hamilton while HRT's Australian Daniel Ricciardo faces a largely meaningless five-place penalty for an unscheduled gearbox change.
Vettel will be joined on the front row by Australian team mate Mark Webber because McLaren's Lewis Hamilton, who was second fastest in the final session, has a three-place penalty for ignoring warning flags in Friday practice.
Lewis Hamilton's hopes of clinching his third Formula One world title at the US Grand Prix here in Texas were boosted when Sebastian Vettel, his closest rival, said he would have a 10-place penalty on the starting grid.
He had been the 16th fastest driver in qualifying, but a five-place punishment for Romain Grosjean over a gearbox issue and a three-place penalty incurred by Carlos Sainz proved to be good news for Palmer.
