Following a tepid and dull first half at the Gewiss Stadium in Bergamo, the Gunners conceded a penalty just three minutes into the second period, as Ederson breezed past Thomas Partey before being felled by the Ghanaian.
Clement Turpin's initial penalty decision was upheld following a VAR check that lasted a good couple of minutes, and Mateo Retegui stepped up to the 12-yard mark in front of the Atalanta ultras.
However, Raya guessed correctly to keep out the Italy striker's initial penalty, diving low to his right and parrying the ball back into the air, which would seemingly offer Retegui a simple tap-in.
The Atalanta forward and Gian Piero Gasperini were left dumbstruck, though, as Raya astonishingly managed to claw his header off the line before Arsenal scrambled the ball behind for a corner.
The Spaniard was immediately mobbed by his ecstatic teammates as a couple of bottles rained down from the Atalanta stands, and speaking on TNT Sports, Robbie Savage labelled his second save one of the best he had ever seen.
Raya's double save in Bergamo comes just a few weeks after a similarly astounding reaction stop against Aston Villa, where a deflected Amadou Onana strike smacked the crossbar before he incredibly sprung back up to keep out Ollie Watkins's follow-up.
The former Brentford man - whose penalty heroics also played a massive part in Arsenal beating Porto in the 2023-24 Champions League last 16 - has conceded just one goal in his first four Premier League games this season and won the Golden Glove last term with 16 clean sheets.