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Marquez, who has a 34-point lead over his two compatriots, sealed pole with a stunning lap of 1min 47.804sec to edge out defending world champion Lorenzo by just one hundredth of a second.
"It was a very hard fought qualification," 20-year-old Marquez told Spanish TV sation Telecinco.
"On the second lap with new tyres I was able to get a bit more and lower my time to give me the pole, but tomorrow (Sunday) is what is important and where we will get points for the championship.
"We need to try and have a great race in front of our fans. It will be important to manage the tyres well."
There was frustration for Lorenzo as he had provisionally taken the lead seconds before Marquez made his surge for the line.
However, having come from behind Marquez to win the past two races in Britain and San Marino he is still confident of success on Sunday.
"I am very happy because the truth is I didn't expect a 1min 47sec lap, to do that on this circuit is incredible.
"I made a slight error on the first corner which lost me a few tenths but second place is very good for tomorrow."
Indeed the times set by Marquez and Lorenzo smashed Casey Stoner's previous track record by eight tenths of a second as six riders in total broke the Australian's time set back in 2011.
Pedrosa had been the first to break the record as he set the pace early on and he was disappointed not to have gone faster in his second lap than in his first.
"After the first lap I had a good time and I hoped to go a bit better in the second, but I couldn't.
"In any case the front row is good and we need to fight in the race tomorrow."
There was a familiar feeling for seven-time world champion Valentino Rossi as he qualified fourth behind the Spanish trio and will start on the second row in fourth alongside Stefan Bradl and Alvaro Bautista.
Final qualifying times on Saturday for Sunday's Aragon motorcycling Grand Prix at Motorland on Sunday:
MotoGP:
1. Marc Marquez (ESP/Honda) 1:47.804, 2. Jorge Lorenzo (ESP/Yamaha) at 0.010, 3. Dani Pedrosa (ESP/Honda) 0.153, 4. Valentino Rossi (ITA/Yamaha) 0.158, 5. Stefan Bradl (GER/Honda LCR) 0.324, 6. Alvaro Bautista (ESP/Honda) 0.498, 7. Cal Crutchlow (GBR/Yamaha) 0.849, 8. Bradley Smith (GBR/Yamaha) 1.050, 9. Andrea Dovizioso (ITA/Ducati) 1.415, 10. Aleix Espargaro (ESP/Aspar) 1.544
Moto3:
1. Alex Rins (ESP/KTM) 1:58.571, 2. Maverick Vinales (ESP/KTM) at 0.702, 3. Alex Marquez (ESP/KTM) 0.711, 4. Philipp Oetl (GER/KTM) 1.335, 5. Efren Vazquez (ESP/Mahindra) 1.361, 6. Jonas Folger (GER/Kalex KTM) 1.585, 7. Miguel Oliveira (POR/Mahindra) 1.650, 8. Luis Salom (ESP/KTM) 1.704, 9. Arthur Sissis (AUS/KTM) 1.766, 10. Jakub Kornfeil (CZE/Kalex KTM) 1.791
