Fellow Spaniard Lorenzo pushed Marquez hard, but came home 0.108 seconds slower while Ducati’s Andrea Iannone was third.
"In the first run I felt very good and although I didn’t push myself 100 percent I felt I could improve,” Marquez told reporters.
“The time was a big surprise, the second lap I made a few mistakes and then on the final (lap) I tried to push myself to the maximum and it was too much.”
Last year’s race winner Lorenzo is well placed as he resumes his battle for this year’s championship title with Yamaha team-mate Valentino Rossi, who qualified sixth, 0.857 seconds off the pace.
"I have still got doubts in some areas and I’m not completely confident in braking,” Lorenzo told reporters.
“Marc was very fast but I got close to him in the end and to be on the front of the grid is good.”
Rossi leads the championship on 247 points with Lorenzo 23 points behind. Marquez has 184 points with five races to go.
(Reporting by Tim Hanlon in Barcelona, editing by Toby Davis)
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