Yamaha rider Lorenzo’s time of one minute 37.910 seconds was a pole record for the circuit and his first top slot since Misano last September.
In soaring temperatures he finished 0.39 seconds ahead of Honda's Marquez, who broke his finger in a training accident last week, while Ducati's Andrea Iannone will be third on the front row of the grid for Sunday’s race.
Italian great Valentino Rossi, who tops the world championship standings with 66 points after two race wins, qualified fifth for Yamaha.
"A lot of people said that I had a crisis and I was down, it was one of my worst moments, but just two days later I rode this impressive lap time," said Lorenzo.
"Setting the new pole position record is unbelievable. I rode many impressive lap times in my career, but this one is very special."
Lorenzo, twice a MotoGP world champion, has failed to make a podium finish from the three races so far.
(Writing by Tim Hanlon in Barcelona, editing by Pritha Sarkar/Alan Baldwin)
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