Marquez opted for a hard front tyre even though most of the other riders went for medium, and it seemed to be paying off early on in the race as the Repsol Honda rider was in third place.
Things began to go downhill for the Spaniard soon after as he was passed by teammate Dani Pedrosa and then he struggled to keep up with the top three riders, which also included the Movistar Yamaha pair of Valentino Rossi and Jorge Lorenzo.
"Today's race was complicated and it was perhaps not one of my better days," Marquez said. "I went out with great desire and I felt strong, able to recover the ground I had lost in the first few laps and close in on Valentino and Jorge.
"Then I saw I had problems with the front tyre, because I was losing it a lot."