Marquez withdrew from Sunday's German Grand Prix after suffering his fifth crash of the weekend in the warm-up session.
The crash left him with a small fracture on his thumb, though he was declared fit to race by the MotoGP medical team.
Marquez missed three rounds through injury after a crash in Portugal and has yet to see a chequered flag in a grand prix, while his best result remains a podium in the Algarve sprint race.
When asked about Marquez, Quartararo offered: "It's difficult for him because I can totally understand that since 2020 with the injury… he's been on the podium since, of course.
"But, for me, he's the best. I have no words about him. He's giving his 100% all the time.
"Who crashes five times just to try to be better, to try to be on top?
"He's mentally one of the strongest here, and one moment has arrived where you get injured.
"He broke his thumb this morning, so I can understand he's pushing himself to the maximum. It's strange to say this, but congratulations for what he is doing."
Quartararo has endured similar struggles on the Yamaha in 2023, with the 2021 world champion scoring just one podium so far.
As such, he says he can "understand" Marquez's situation and believes the rest of the paddock does too.
"The thing is we check a little bit with what we have," he added. "The Honda is turning a little bit better than us, but on braking we are a little bit better than them.
"So, this can avoid the crashes a little bit. But you are on the limit all the time, and especially here I could not show the potential.
"Since the beginning of the year we are having tough moments and I can understand Marc 100%, and I think everyone here can understand it."
Quartararo struggled to 13th in the German GP on Sunday having gambled on running a soft tyre while the majority of the field went with the medium rear.
While admitting this was an error, he concedes that his potential was no higher than 10th, and so taking a risk was worthwhile.
"To be honest, when I see the position we were, I wanted to try the soft tyre," he said of his race on Sunday.
"Totally wrong because from lap one basically, I needed a little bit more grip for the first laps and actually I didn't have more grip.
"The tyre was dropping so much. Wrong decision with the tyres, but to finish P10 or P13 is not a big difference. [Potential of the medium] was P10, but not more."
