Wholesale changes from the Gunners saw Cedric Soares, David Luiz, Hector Bellerin, Rob Holding, Joe Willock and Mohamed Elneny handed a start from the win over West Bromwich Albion.
Furthermore, a late change seconds before kickoff resulted in Reiss Nelson entering for Gabriel Martinelli who almost handed Arsenal the lead with a shot from the edge of the area.
Newcastle stayed on the edge thereafter when a ball from Luiz released Pierre-Emerick Aubameyang in a promising area, but he had his volley repelled before Willian skied the follow-up.
Following a lukewarm closing quarter in the first half, the Magpies attempted to spark the encounter into life with the arrival of Matt Ritchie in place of Jamaal Lascelles.
This indeed fired up the visitors, who threatened the opener through a looping strike from Andy Carroll before the latter fired in a half-volley seconds later.
Arsenal started to regain confidence as the closing quarter of the second half approached and had Martin Dubravka scrambling around his area to thwart a downward header from Willock.
The two sides went at each other in the final minutes, with a first-time shot from Kieran Tierney flying wide before Jeff Hendrick send a cross from Ritchie well off target.
As the match entered extra-time, the Gunners broke the deadlock in the 109th minute with a first-time finish near the shoulder of the area from Emile Smith Rowe.
The Gunners put the result to bed when Aubameyang arrived in the centre of the area to help a low cross from Tierney past Dubravka, as it finished 2-0 on the night.