The home side started brightly, with debutant Joelinton heading wide before Jonjo Shelvey hit the post.
Arsenal's best chance of the first half fell to Henrikh Mkhitaryan, who shot over the bar when well placed inside the penalty area.
The Gunners made the breakthrough after 58 minutes, with Ainsley Maitland-Niles's pass finding Aubameyang, who lifted the ball over Martin Dubravka to score.
Unai Emery handed Premier League debuts to Dani Ceballos, Nicolas Pepe and Gabriel Martinelli during the second half as Arsenal held on to make it 13 wins from 14 competitive matches against Newcastle.
Newcastle: 17 Aug v Norwich (A)
Arsenal: 17 Aug v Burnley (H)
Referee: Martin Atkinson; Assistants: Lee Betts, Constantine Hatzidakis; Fourth official: Darren England; VAR: David Coote; Assistant VAR: Nick Hopton