
England winger Saka put the Premier League leaders ahead in the 32nd minute at the Fortuna Arena after Gabriel’s header hit Slavia captain Lukas Provod’s raised hand and a VAR review confirmed the handball.
Merino, replacing Swedish striker Viktor Gyokeres who was injured at the weekend, made it 2-0 on the volley after 36 seconds of the second half after a cross from the unmarked Leandro Trossard.
He put Arsenal 3-0 ahead in the 68th minute with a header flicked past goalkeeper Jakub Markovic after Declan Rice lofted the ball into the area.
Arsenal, who brought on 15-year-old Max Dowman in the second half to become the youngest-ever player in the Champions League, have not conceded a goal in eight successive matches in all competitions – equalling a club record set in 1903.
Slavia are still without a win in the league phase and remain on two points.