Despite starting from pole at the Aragon Grand Prix in Spain, things started to go wrong for the French-man after the first three laps when he lost the tyre pressure in his front wheel and ended outside the points in 18th place.
Only the top 15 riders earn championship points. The only positive for Quartararo was that his title rivals also failed to fully capitalise on his bad luck.
Nearest challenger and new leader Joan Mir of Spain came in third behind Alex Marquez with Alex Rins winning the 23-lap race.
“Today was a disaster but it could have been even worse if Mir had won, Maverick (Vinales) came in second, Andrea (Dovizioso) third.
“In our negative, we need to think about the small positive we had today, which is that both Alexes finished in front of Joan. The championship is surely not over yet.”
Mir now leads with 121 points although he has yet to win a race. Quartararo, who was the leader in the previous nine rounds, drops to second with 115 while Vinales and Dovizioso lurk behind with 109 and 106 respectively.
Quartararo hopes the team will fix the problem with the bike soon before the second race at the same venue this weekend.
“We need to find out why the front pressure went totally out of control, that’s not normal.
“It’s so strange. We had the pace to fight for, I will not say victory or podium, but the top five or six.
“That would have been great but like I said, the front tyre just went out of control and we don’t know why.
“I couldn’t brake, couldn’t turn, couldn’t lean the bike. That’s the reason why I was going so wide and couldn’t stop the bike.
“It’s difficult to understand and the team are now looking into it and for sure we need to see exactly what was the problem, which for me was only the pressure of the front tyre.”