The Mexican was firmly down on the fastest time in the session before the incident, as was team-mate Max Verstappen, before Perez's crash through Variante Alta ruined that particular lap for both Red Bulls.
It meant a race against time for Red Bull to be able to make the necessary repairs to Perez's car ahead of qualifying later on Saturday, with the 34-year-old's car left with heavy damage at the front.
Red Bull woes continue
Following a Friday in which a lack of pace and uncharacteristic mistakes from three-time world champion Verstappen caused a bad day for Red Bull, Saturday saw the pair looking much more comfortable.
Verstappen had called his car 'a catastrophe' in FP1 as the Dutchman lost his temper at various points, but seemed to be happier during Saturday's practice session.
However, Perez added to what has been a miserable weekend so far with his crash, which is likely to hamper his weekend, and meant that team-mate Verstappen could not improve on sixth place in the timings.
It follows a weekend last time out in which Red Bull were comprehensively beaten by McLaren in Miami, and arrived at the Emilia-Romagna GP weekend hoping to bounce back.