Alexandre Lacazette's beautiful free-kick after 36 minutes lifted the Gunners to a 3-0 aggregate advantage. Napoli offered little in response.
In Arsenal's native London, Chelsea made hard work of a 5-3 aggregate ousting of Slavia Prague. Maurizio Sarri's side fashioned a 4-1 lead by the interval, but a Petr Sevcik brace in the second half gave the visitors slim hopes of a remarkable comeback.
Elsewhere, Eintracht Frankfurt beat Benfica 2-0 at Waldstadion to advance on away goals following the Portuguese club's 4-2 victory in the first scuffle. Sebastian Rode jabbed in the decisive goal from the edge of the area after 67 minutes.
Arsenal will face Valencia and Eintracht will take on Chelsea in the semifinals.