Joao Pedro scored twice late on as Brighton avoided an FA Cup upset at Championship side Stoke with a 4-2 comeback win.

The hosts – who had not beaten top-flight opposition in the competition since they reached the final in 2011 – had held the lead for 35 first-half minutes courtesy of Jan Paul Van Hecke’s own goal, after which Steven Schumacher’s team were the better side.

However, Brighton’s Ecuador left-back Pervis Estupinan let fly from 20 yards in the final minute of six added on before the interval and captain Lewis Dunk headed last season’s semi-finalists ahead just after the break.

Dunk’s raised arm conceded the penalty from which Lewis Baker equalised and it needed Pedro’s 14th and 15th goals of the season to see the Premier League team through in the final 19 minutes.

Schumacher is only five matches into his reign in the Potteries and this was his first defeat – although he has had four draws – but the way his players took the game to opponents 32 places above them offers hope for the 19th-placed second-tier club.

After Pedro’s early deflected shot looped just wide of the post the momentum was all Stoke’s with Mehdi Leris forcing the first save from Bart Verbruggen, one of four changes made by Roberto De Zerbi.

It was from that right-hand channel that Stoke took the lead as Dunk’s intended pass for Pedro was intercepted by Ki-Jana Hoever, stepping out from centre-back, and he slid in South Korean midfielder Bae Jun-ho, whose low cross was turned in by Van Hecke.

The 21-year-old Hoever, performing a hybrid role as the third centre-back stepping into midfield, was at the heart of all Stoke’s best play and twice set up Wesley, who curled wide and headed straight at Verbruggen.

But just seconds from the break goalkeeper Daniel Iversen, making his debut after signing on loan from Leicester 24 hours earlier having not played for the Foxes, was beaten by Estupinan’s drive and the advantage swung to Brighton.

Dunk had been a threat from set-pieces and he headed home Billy Gilmour’s far-post cross just moments after Daniel Johnson and Sead Haksabanovic both got in each other’s way as they ran onto Hoever’s inviting cutback.

Stoke responded with Wouter Burger’s 25-yard shot, turned behind by Verbruggen, and from the resulting corner substitute Luke McNally’s header hit the raised arm of Dunk, who knew little about it but had no VAR to save him and Baker drove home from the spot.

At that point the game could have gone either way but Brighton’s greater experience told as Pedro headed in Pascal Gross’ cross and then converted Van Hecke’ square pass as the visitors made it past the third round for the seventh time in eight seasons.