The championship leader had his right leg run over by KTM's Brad Binder in a horrible accident in last week's Catalan GP.
Though he was cleared to ride, Bagnaia struggled with the pain in his leg in Saturday's 13-lap sprint race and only narrowly fended off the KTM duo of wildcard Dani Pedrosa and Brad Binder for third.
Bagnaia says his defence of Pedrosa into Turn 1 on the last lap was one of the hardest braking moves he has ever made because it was "too important" to get onto the podium after what happened last week.
"He [Pedrosa] was pushing a lot, I was hearing him," Bagnaia, whose points lead has been cut to 45, said.
"The braking I did in the first corner on the last lap was one of the hardest for sure, because he was already in front of me and it was too important to restart with a podium from [what happened in] Barcelona. Much more than this was very difficult."
Expanding on how he felt physically in that race, Bagnaia said: "Quite bad, right now. Tired, really tired. I need some rest for sure.
"But we were expecting it, I was expecting it and the soft rear tyre was not an easy solution for the race because it made the bike more nervous, it was shaking more, and it was difficult to have a rhythm.
"In any case, I'm happy with the result considering where we were six days ago. I'm so pleased and proud for the result we achieved."
Bagnaia says he needs a stronger painkiller for Sunday's full-distance grand prix to be able to focus more on riding and not where to place the foot on his injured leg.
"For tomorrow, for sure, the main thing will be to increase the painkiller just to have a clearer idea on just riding and not thinking on where to put my foot, because today in the first two, three laps I was struggling on leaning the knee because I was not warmed [up]," he added.
"But then the pace was quite good. I was struggling with the front because it was difficult to stop the bike, but I was expecting it.
"For tomorrow it will be better because we go with the medium. Right now I will re-watch the race to understand what [race winner Jorge] Martin is doing in the last sector, for sure."
Fellow VR46 Academy rider Marco Bezzecchi finished second in the Misano sprint also carrying injury, having hurt his left hand in the Turn 1 pile-up instigated by Enea Bastianini in Barcelona.
Bezzecchi chased eventual sprint winner Martin hard in the early stages, but admits the pain in his hand ultimately conditioned his pace in the second half of the race.
"Now, not very good, but happy," he said. "At the beginning to be honest I felt incredible. I don't know if it was the adrenaline of the start, the painkiller also helped. But in the beginning I was catching Jorge.
"Then once I got close to him I started to have a bit of pain, especially in change of direction. So, in sector one I made some mistakes and lap by lap I was losing a bit.
"Some laps I was able to fight, but in some other laps I was making some mistakes, missing a bit of power to move the handlebar from left to right.
"Maybe from the second half, but I really suffered in the last three laps. A lot of pain."
Additional reporting by Lorenza Dadderio
