The Gunners finally broken their visitors resistance after the 100 minute mark with crucial goals from Emile-Smith Rowe and Pierre-Emerick Aubameyang.
Arsenal looked bright and breezy in the opening stages with Reiss Nelson and Nicolas Pepe testing Martin Dubravka.
But despite the positive start in North London the game descended into a slug fest after the break with half chances for Willock and Andy Carroll.
The introduction of Smith-Rowe tipped the balance for Arsenal in the extra 30 as the England U20 international superbly fired home.
Newcastle threw the kitchen sink at it in the final minutes but Arsenal wrapped it up in last few seconds as Aubameyang tucked home his first goal in over a month.
Full Time at the Emirates Stadium it’s Arsenal 2 Newcastle 0