The Dutch champions had to play the final quarter with 10 men when Pereiro was sent off for barging his fellow Uruguayan Diego Godin to the ground, his second bookable offence coming after 68 minutes.
Pereiro could have few complaints as he had just received a final warning from Italian referee Daniele Orsato, and after that it was a backs-to-the-wall exercise for PSV, who retreated ever deeper to keep Atletico at bay, with the return leg in Madrid in mind.
PSV were a surprise last-16 package after knocking out Manchester United at the competition’s group stages.
But Atleti predictably proved a far tougher nut to crack, with Diego Simeone’s 2014 finalists having forged a reputation as one of the best defensive units in Europe.
Atleti had conceded only three goals in six games in winning their Champions League group and goalkeeper Jan Oblak had just one save to make in keeping yet another clean sheet for the Spaniards.
Huge roars greeted the final whistle and PSV will feel they are capable of causing an upset at the Vicente Calderon in the March 15 return.
Zoet, Arias, Bruma, Moreno, Willems, Narsingh (Isimat-Mirin 65), van Ginkel, Propper, Guardado (Hendrix 74), Locadia (Lestienne 85), Pereiro.
Pasveer, Schaars, Jozefzoon, Brenet.
Oblak, Juanfran, Savic, Godin, Filipe Luis, Oliver Torres,Gabi,Saul (Correa 74), Koke, Griezmann, Vietto (Fernando Torres 61).
Moya, Kranevitter, Fernandez, Jesus Gamez, Gimenez. Booked: Savic.
Daniele Orsato (Italy).