Rizwan and Irfan both suffered hamstring injuries in the third match in Rawalpindi
French centre back Kounde opened the scoring in the 25th minute, dribbling from his own area and playing a one-two with a team mate before bursting past four Barca players to confidently slot past Marc-Andre ter Stegen.
The Barca keeper made a superb save to prevent Sergio Escudero doubling Sevilla's lead at the end of the first half but Croatia midfielder Rakitic made sure of the victory with a thumping finish into the roof of the net in the 85th minute.
Lionel Messi could have snatched a late away goal but was thwarted by Sevilla keeper Bono and Julen Lopetegui's side saw out the win without conceding to take a big advantage into the second leg at the Camp Nou on March 3.