Marquez had topped all four practice sessions heading into British Grand Prix qualifying, but his initial Q2 lap was underwhelming - placing the Honda only third behind Dovizioso's Ducati and Lorenzo's Yamaha.
That was just a warm-up effort, though, and Marquez's next lap put him on provisional pole by three tenths of a second.
His rivals responded, and Lorenzo - who had been off the pace and extremely unhappy with Bridgestone's Silverstone tyre choice on Friday - stole the top spot back again with a 2m01.175s lap.
It wasn't enough, as Marquez's final effort was a 2m00.829s, giving him pole while Dovizioso edged out Lorenzo by 0.035s for second place and his third straight front row start.
Aleix Espargaro put the Forward Yamaha ahead of Dani Pedrosa and Valentino Rossi on row two.
Bradley Smith was top Briton in seventh, though it was Scott Redding who made the biggest impression among the home contingent as he topped Q1 on his production-spec Gresini Honda and then held seventh after the first Q2 runs. He was eventually pushed back to 11th.
Stefan Bradl added an accident in practice four to his Saturday morning accident and could only qualify ninth, just in front of fellow crasher Andrea Iannone, who fell on his final qualifying lap.
Briton Leon Camier also had a shunt in qualifying, going off on his last Q1 run and leaving himself 18th on the grid.
Cal Crutchlow could not get beyond Q1 and will start 15th for his home event.
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