Hamilton was a third of a second faster than his teammate and championship leader Nico Rosberg as Mercedes again dominated the front row.
Hamilton's first time in the final session of qualifying was deleted for exceeding track limits as he ran wide at the famous Copse Corner, but he returned to pick up the 55th pole of his career.
"There was a lot of pressure on that last lap but I knew I couldn't let those guys down," said Hamilton, who is bidding for a hat-trick of wins at Silverstone.
"It wasn't the best day out there for me. Congrats to Lewis. Tomorrow there is all to play for," was the reaction of Rosberg, who has a narrow 11-point lead in the standings.
It looks set to be another showdown for the top step on the podium between the Mercedes pair, just a week after they collided on the final lap of the Austrian Grand Prix.
Hamilton went on to win, with Rosberg slipping to fourth place, but the incident led to furious team boss Toto Wolff threatening to impose team orders on his drivers.
Red Bull pair Max Verstappen and Daniel Ricciardo will occupy the second row, with the Ferrari pair of Kimi Raikkonen and Sebastien Vettel setting the fifth and sixth best times.
But Vettel will only start 11th on the grid after being given a five-place penalty for a changed gearbox.
Teenager Verstappen, who secured a famous maiden victory in Spain when Hamilton and Rosberg crashed out after colliding with each other, conceded it might need a similar incident again for him to come through.
"We are strong compared to cars behind us. It seemed like the Mercedes had a turbo button," he said.
Two-time champion Fernando Alonso continued McLaren's improvement by making the top 10 final session of qualifying, but like Hamilton had a lap time deleted for exceeding track limits, this time at the final corner.
His teammate Jenson Button, an encouraging sixth in Austria, was eliminated in the first session of qualifying after his rear wing came loose.
McLaren decided not to send him out for a second run to the disappointment of the home crowd, leaving Button 17th on the grid.