The Mexican got through Q1 in fifth place and was fourth in Q2 before earning fifth spot in the final session, having struggled throughout to match the pace of team-mate Max Verstappen.
As the second occurrence of Pirelli’s alternative tyre allocation, with fewer sets and compulsory use of hard, medium and softs across the three qualifying segments, Monza was difficult for all drivers.
However, Perez made his own life difficult with a spin into the Parabolica tyre wall that saw him miss some crucial laps at the end of FP2.
It also had a knock-on effect into FP3, when he ran limited laps. After an oil leak curtailed his session, he had to undergo a power unit change, with the team putting in a previously used example for qualifying.
Asked if he was happy to have salvaged fifth place, Perez insisted: "Yes, considering the situation, missing FP3, basically going blind, I didn't run new tyres today before qualifying, and it wasn't an ideal day,” he said. “But it is what it is.
“I think given how small the margins were, our preparation was not ideal. We had a lot of pace yesterday, I think yesterday was looking great. But unfortunately, we didn't get to show what we were able to do today."
Perez clarified that the crash was "not really" a setback other than its impact on track time.
“This sort of thing can happen. It just disrupted the situation for us in terms of just having issues with the setup of the car for this morning.
"And unfortunately, we had issues also with the engine, so we had to change it. Yeah, it was a little bit too much."
He conceded that it’s not easy to optimise the car for the three tyre compounds that were used in qualifying: "It's quite tricky, especially if you have an issue like I did, you go completely blind, and the first time you run the soft tyres is in Q3, and you are always a step behind."
Perez now hopes he can stay clear of any first-lap trouble.
"Well, the further up you are the better,” he said. “I'm in the third row, so hopefully I can get into the second row.
"I don't want to go all the way to the lead, but obviously I want to get in some positions, and hopefully tomorrow we can do it.
“It will be crucial for us tomorrow to be able to go with the pack, not to lose any race time, not to use the tyres more than we want.”
Intriguingly, he discounted the suggestion that Ferrari won’t have the race pace with which to fight on Sunday: "Well, it's not what we've seen so far. But let's see tomorrow. I think it's a long race ahead."