Kounde ran from his own penalty area, beat four Barca players and confidently fired past Marc-Andre ter Stegen.
Rakitic - who left the Nou Camp at the end of August after winning 11 trophies with Barca - made sure with a thumping finish into the roof of the net.
Lionel Messi could have snatched a late away goal but was denied by Bono.
Julen Lopetegui's side saw out the win without conceding to take a big advantage into the second leg at the Nou Camp on 3 March.
Athletic Bilbao - who could win the yet-to-be-played 2019-20 final in April
- are in the second semi-final against Levante.