Pedrosa on pole for Catalunya MotoGP
Spanish rider Dani Pedrosa pulls a wheelie during the Moto GP third free practice session of the Catalunya Grand Prix at the Montmelo circuit near Barcelona, on June 13, 2014 - by Josep Lago
It was the 45th pole position for the former 250cc world champion and his 26th in MotoGP as he timed 1min 40.985sec to outpace compatriots Lorenzo, by 0.115sec, and Marquez, who is chasing a seventh straight victory, by 0.150sec.
Pedrosa's performance ended the pole position winning streak of Marquez, who walked away from a crash towards the end of the session, and will be the first time since Motelgi last year Marquez will not start at the front of the grid.
Marquez became the first rider since Italy's Valentino Rossi in 2002 to win six successive races, when he edged out Lorenzo at the Italian Grand Prix at Mugello on June 1.
He will carry a healthy 53-point lead over Rossi into Sunday's race at the Montmelo circuit while Pedrosa is just one point further back in the championship standings.
Germany's Stefan Bradl will lead the second row as he finished fourth fastest at 0.235sec on a Honda LCR, with Rossi alongside him, 0.305sec slower than Pedrosa.
Another Spaniard, Aleix Espargaro, who was fastest in Friday's practice on his Yamaha Forward, completes the second row.
In qualifying for the Moto2 Grand Prix, Spain continued to dominate the weekend as Esteve Rabat rode his Kalex bike to pole position.
The championship leader recorded his fifth pole of the season, and led home Finnish team-mate Mika Kallio by 0.571secs with fellow-Spaniard Maverick Vinales completing the front row 0.623sec back, also on a Kalex.
Earlier, Marquez's younger brother Alex set a course record as he rode his Honda to pole position for the Moto3 Grand Prix with a time of 1min 50.232sec.
The 18-year-old finished his fastest lap a comfortable 0.618sec quicker than Italian KTM rider Enea Bastianini.
Spaniard Alex Rins, on a second Honda, was a further 0.062sec back to round out the top three.