Andrea Belotti and Paulo Dybala scored in a seven-minute spell in the first half to seal the win.
Six-time champions Sevilla lost 2–0 to PSV Eindhoven in the Netherlands but went 3–2 on aggregate.
Luuk de Jong and Fabio Silva scored late goals for the Dutch side, who sent off Mauro Júnior in stoppage time.
Sporting Lisbon were also among the winners, a 4–0 victory in Midtjylland followed by a 5–1 win in Denmark.
Riding high in the Bundesliga, Union Berlin beat Ajax 3-1 last week after the first leg ended goalless.
Robin Noche, Josip Juranovic and Danilho Doekhi scored as Union won their first ever Europa League knockout stages.