Sevilla soon settled and went close themselves – Kounde's first-time effort from 20 yards spinning just wide.
But the young Frenchman found the target five minutes later, the centre-back cheekily nutmegging Samuel Umtiti on the edge of the Barca box after a trademark buccaneering run before firing past Marc-Andre ter Stegen.
The German goalkeeper showed his class to keep the score 1-0 just before half-time, pushing Sergio Escudero's ferocious goal-bound effort over.
Umtiti made a vital intervention to deny Youssef En-Nesyri a one-on-one opportunity early in the second 45, and soon after Bounou once again thwarted Messi, turning his effort around the post.