It was Lorenzo's second pole of the season and he beat Italian team mate Andrea Dovizioso by 0.159 of a second.
Yamaha Tech3's French rider Johann Zarco completed the front row in the tricky conditions, with Britain's Cal Crutchlow fourth fastest for LCR Honda.
Avintia Ducati rider Tito Rabat was taken to hospital with a suspected broken leg after being hit by Franco Morbidelli's Marc VDS Honda following a fall in the day's wet and treacherous final practice.
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Marquez leads Italian Valentino Rossi, who starts a distant 12th, by 59 points ahead of Sunday's race at Silverstone.
(Reporting by Alan Baldwin, editing by Ed Osmond)
