The reigning world champion improved his time on his final lap, setting a benchmark of one minute 10.736 to take his 11th pole of the season, the 60th of his career - just eight off Michael Schumacher's record. It was also Mercedes' 19th pole this year - a new Formula One record.
Nico Rosberg was a tenth of a second behind Hamilton, despite beginning his lap quicker.
The gap to the rest of the field was bigger, with third place Kimi Raikkonen nearly seven tenths of a second behind the pole position time. He beat Max Verstappen into fourth with a last gasp time, while his Ferrari team mate Sebastian Vettel was fifth fastest.
The Ferrari drivers' qualifying performances have been evenly split 10-10 this season.
Valtteri Bottas missed out on the final part of qualifying, he will start the Grand Prix in 11th, ahead of Esteban Gutierrez and Felipe Massa in the other Williams who endured his worst home qualifying result in what is his final F1 appearance on home soil.
Jenson Button was a major casualty from first qualifying. He will start 17th after balance issues, with Kevin Magnussen, Pascal Wehrlein, Esteban Ocon, and the Saubers of Marcus Ericsson and Felipe Nasr completing the field.
Bahrain International Circuit - Winter testing