For only the second time since stepping up to the premier class, Marquez forced to take part in Q1 on Saturday ahead of the Italian GP at Mugello.
Needing to finish in the top two in order to enter Q2, the Repsol Honda rider could only produce the third fastest time and as a result will start Sunday's race from 13th on the grid.
Speaking after qualifying, Marquez said that the decision to stick with an old tyre in FP3 cost him dearly.
“We can say that we did a mistake in FP3, that I didn't put on a new tyre [at the end]. I used a tyre from yesterday from the beginning until the end because we were thinking too much about working on the electronics. And to work on the electronics you need [many] laps on the tyre," he explained.
“So we concentrated on that and then I go to Qualifying 1. In Qualifying 1 I had the confidence to push only on one tyre, but we had another problem.”
While optimistic about his chances of challenging for a podium finish, Marquez conceded that the day had been bitterly disappointing.
"We can't be happy about today, because this was the worst qualifying result that we have had in MotoGP," he said.
The Spaniard added: "I think we have a good pace for tomorrow, although it is clear that starting from so far back we will suffer a lot," said Marquez.
"We will try to make a good start and opening few laps to get into the leading group."