Perez was sent out of the Red Bull garage during a red flag break to recover the abandoned car of Kevin Magnussen, but having claimed the spot at the head of the queue at the exit he had to wait longer than the team had anticipated for the session to resume.
In the meantime, he lost tyre temperature, and after a frantic final run, he finished the session in 16th place. He subsequently gained a spot from a penalty for Valtteri Bottas.
Silverstone is the fifth race in a row where Perez has failed to make it into Q3.
"I think the red flag lasted longer than we predicted initially and that didn't help for the temperature of the tyres," he said when asked about the session by Motorsport.com.
"It's just a shame to lose out, because we had a great Friday, the race pace was looking really good. So I think starting from the back it's going to be another race where we will try to minimise the damage."
Perez admitted that dealing with cool weather and a track transitioning from wet to dry is not his strength at the moment.
"I think in these conditions is where I struggle the most with the car," he said. "My issues with the car become more apparent in the changeable conditions.
"So I think it's something that as a group we need to get on top of and understand what we are able to do better and yeah, simple as that."
Red Bull advisor Helmut Marko conceded that tyre temperature was an issue.
"We wanted to have him [on track] as soon as possible because there was always the chance of rain," he told Austrian TV.
"The fact that it then took so long to recover [Magnussen's car] that his tyres cooled down completely wasn't taken into account. That was one of the reasons why he didn't reach the optimum on that lap."
Marko added: "He needs to improve his qualifying in general. This is not the first time. But he has the bonus of always delivering pretty good races.
"Here we have a race track where you can overtake. With our DRS advantage, it should be possible for him to finish well in the points again."
