Perez's time came with 50 minutes to run, laying down a 1:30.305s to move more than three-tenths clear of next-best Lewis Hamilton.
The Mexican had been just 0.048s quicker than Hamilton before setting three purple sectors just inside the final hour – a time that would have been good enough for pole at last year's Bahrain Grand Prix by more than 0.2s.
Perez used a set of C4 tyres on his best lap, versus the C5 – one step softer in Pirelli's range – for Hamilton.
Third fastest was Valtteri Bottas who mustered a 1:30.827s for Alfa Romeo Sauber with just under 40 minutes left in the day.
The Finn's effort built on the foundations laid by team-mate Zhou Guanyu on Friday when the Chinese driver ended the day fastest.
Bottas had used a set of C5 tyres for his effort, which left him just two-tenths adrift of Hamilton's effort.
The time also came after 120 laps of running as Alfa Romeo Sauber fielded only the 10-time grand prix winner throughout the day's two sessions.
Bottas' time demoted the Ferrari pairing of Charles Leclerc and Carlos Sainz, who had sat third and fourth best respectively – the former's effort having stood the test of time from the morning's running.
However, both were more than seven-tenths away from the outright pace on a day Leclerc suggested his team had “work to do” to catch Red Bull.
Perez was prolific in the final four hours in Bahrain, wracking up well over 100 laps as his personal mileage across the three days surpassed 1000km.
It was another difficult session for McLaren, with Lando Norris spending a prolonged period in the garage as the team worked on the wheelbrows on his car.
He'd managed less than 20 laps in the first three hours, finally emerging with scarcely more than 45 minutes remaining in the test.
Norris ended Saturday's running with the lowest mileage of any of the regular race drivers – only Felipe Drugovich managed fewer laps though the Brazilin had only two sessions of running versus the McLaren driver's three.
There was again strong running for Williams with Alex Albon mustering north of 130 laps, the most of any driver over the course of the day.
He was one of just three drivers to drive throughout Saturday, the others being Perez and Bottas.
Again the final 15 minutes of the session were set aside for systems tests, with a Virtual Safety Car and red flag followed by a Safety Car restart that saw Bottas in an energetic mood.
Practice starts then followed as a line was drawn under pre-season testing, with Perez fastest and Red Bull firm favourites heading into the 2023 season, which gets underway in less than a week.