Marquez takes sixth pole of season at Misano
Honda's rider Marc Marquez of Spain celebrates after winning the pole position during the qualifying session of the San Marino Moto Grand Prix on September 14, 2013 at the Misano world circuit in Misano Adriatico.
Honda rider Marquez, who has a 30-point lead over teammate Dani Pedrosa in the title race, was just 24 thousandths of a second faster than reiging world champion Lorenzo.
His time of 1min 32.915sec was a new lap record for the Misano track, bettering Casey Stoner's old mark.
Pedrosa, who took pole last year, was fourth on Saturday, eight-tenths of a second off the pole time.
"I think Jorge and Valentino will be strong on Sunday," said Marquez,who won the Moto2 race at the same track 12 months ago.
"Especially Valentino will be very, very strong. I don't know why, but I just sense that, Jorge also; he will try to recover some points in the championship and we will try to be there."
Lorenzo, who is 39 points off the championship lead, said that Yamaha had work to do despite their double front-row presence.
"I expected to struggle less this weekend and go faster than last year but I couldn't be faster and I couldn't improve the bike so much," said the Spaniard.
"We improved a little but not enough to be closer to Marc. He made an amazing lap. We are struggling to stop the bike in braking and we have more spinning than normal in acceleration, that is why the lap time is not great."
Britain's Cal Crutchlow was fifth and shares the second row with Aleix Espargaro, Stefan Bradl and Andrea Dovizioso.