The 20-year-old Honda rider, who had set the fastest ever lap of the circuit in morning practice, broke Dani Pedrosa's pole record from last year with a time of one minute 30.237 seconds.
He was 0.340 of a second ahead of defending champion and compatriot Lorenzo on a Yamaha, while Honda team mate Pedrosa completed the front row of the grid in third.
Marquez is aiming to oust American Freddie Spencer, who won the 500cc title aged 21 in 1983 with Honda, as the youngest champion in the top class of grand prix racing.
Marquez leads the standings with 318 points, 13 ahead of Lorenzo, the only rival who can catch him and who has cranked up the pressure with victories in the last two races in Australia and Japan.
The youngster was almost thrown off his bike in a high-speed wobble near the end of qualifying and he admitted it had come as something of a wake up call.
"Yes, I had a bit of a scare on my last lap when I had already decided not to push it anymore, but when you aren't completely focused, look what happens," Marquez told Spanish broadcaster Telecinco.
"It was a little warning looking ahead to tomorrow when I will have to be 100 percent focused, and do my race.
"The positive thing is that I am feeling good, and have found my rhythm. Jorge perhaps has a slightly better rhythm so far, but it has been a good outing."
Lorenzo's chances of snatching pole from Marquez faded when he had to change to his second bike after losing power during qualifying.
"The second bike has a much more aggressive engine and is much worse so I wasn't able to compete with Marc for pole, but we still logged a good time," Lorenzo said.
"(The title) is very difficult, 13 points is a big gap. Marc has to finish fifth, sixth or worse, which is hard to imagine but anything can happen in these races, where many factors can effect things. We'll see.
"We have to be very focused and do our jobs as best we can to win the race, and we'll see how it plays out at the end."
Italy's Valentino Rossi leads the second row in fourth place for Yamaha, ahead of British duo Cal Crutchlow and Bradley Smith.
Spanish world champion Pol Espargaro led the way with pole in Moto2 qualifying, ahead of Italy's Simone Corsi and Spain's Jordi Torres.
The end of the Moto3 championship promises to be a thriller with the Spanish trio of Luis Salom, Maverick Vinales and Alex Rins separated by only five points in first, second and third places respectively.
Rins grabbed pole ahead of Salom and Vinales.
(Writing by Mark Elkington in Madrid, editing by Alan Baldwin)
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