The Honda rider had to come through Q1 after failing to get into the top 10 at the end of FP3, but looked very uncomfortable on the RC213V in time attack mode.
Despite this, Marquez produced a 1m58.454s lap at the end of Q2 to put his Honda third on the grid but admits he has no real explanation as to how he achieved this.
“I’m really surprised to be on the front row, especially because… I don’t know,” Marquez said.
“The speed is not there, the feeling is not there. But in qualifying, I was there. So, I cannot explain how and I cannot explain why we are on the front row.
“But the fact is we did two good laps, not only in Q2, but in Q1 I was fast.
“I went out [at the start of] Q2 on used tyres and I was not so bad. And then with the new one I pushed even more.
“I’m happy for this front row, but I believe tomorrow we will struggle more because I’m fighting against the bike.
“I’m fighting against the bike all the time and this is very demanding on physical condition, on the concentration. For race distance the pace is not there, but we will try to do our best.”
Marquez spent both qualifying sessions using Ducati riders as references to help him with the lap time, but on the occasion of his fastest efforts both Jack Miller and Francesco Bagnaia crashed in front of him.
The fact he was able to achieve the lap times he did despite losing his tow was “the biggest surprise” for the Honda rider.
“If you check a bit, all Honda riders were looking for a slipstream because we are losing 0.150s on the back straight and 0.150s on the main straight,” he added.
“So, if you have some slipstream you just gain 03s for free on the straight. When I was Miller crashed in Turn 2, I said ‘ok, this will be difficult’, but I kept pushing and the lap time came. And it was the same in Q2.”
Third in Malaysia marks the six-time MotoGP world champion’s third front row start in the four races since he returned to action last month, and follows on from a podium appearance last weekend in Australia.
Marquez says the way he was able to get the best out of the bike despite having to override it was an even more significant sign than his Phillip Island podium that his recovery is going well.
“It was a very, very, very important day, even more than Australia because here is a circuit that always in the past is not one of my best circuits,” he said.
“I cannot say I was struggling because I won sometimes here, but it’s not one of my favourite circuits.
“I’m struggling on my riding style, even all Hondas are struggling a lot and as we see I’m fighting against the bike.
“For some laps I can, I can ride like I want. But as I say in interviews, I’m feeling better and better and I can absorb some of the problems of the bike trying different riding styles that in the last two years was impossible.
“In Buriram I felt a step, in Australia I felt a bigger step and the most important thing for me was from Australia to here I recovered in a good way and I started the weekend in a good way.”
