Home hope Cal Crutchlow, who fell twice in morning practice, joined the battling Spaniards on the front row with a late quick lap on his non-factory Tech3 Yamaha.
Germany's Stefan Bradl starts fourth on the LCR Honda ahead of Spaniard Dani Pedrosa, Marquez's team mate, with Yamaha's Italian Valentino Rossi completing the second row.
Italian Andrea Dovizioso, who makes his 100th MotoGP start on Sunday, will line up in seventh place.
Marquez will be chasing his fifth successive win on Sunday after becoming the first rookie to win four in a row in the top category.
If the 20-year-old Spaniard wins on Sunday, he will be only the seventh rider in the 65-year history of grand prix racing to take five successive victories in the leading class as well as the youngest.
He secured his fifth pole of the year, and third in five races, with a best lap of two minutes 00.691 seconds on a sunny afternoon at Silverstone.
Lorenzo's best lap on the factory Yamaha was 2:00.819, and the top five times were all within a second.
Spain's Aleix Espargaro missed final qualifying after injuring his neck and a finger in final practice. He will have a medical on Sunday to see whether he can race.
(Reporting by Alan Baldwin, editing by Stephen Wood)
