The 17-year-old was on target either side of efforts from Gabriel Jesus and Kai Havertz as Mikel Arteta's side booked their spot in the quarter-finals with minimal fuss, although PNE did not completely fold and had a few moments of their own late on.
A meeting between the only two clubs in English football to ever go a full season unbeaten, Arsenal settled into a steady period of possession against their Championship foes, whose defensive structure was initially holding out.
However, the trio of Jesus, Raheem Sterling and 17-year-old Nwaneri sought to cause havoc whenever they could, and it was seemingly only a matter of time before the Gunners breached the PNE backline.
True enough, the goal that the visitors' dominance merited arrived through an increasingly rare scorer in Jesus - who had not scored for exactly nine months before the trip to Deepdale - and the two-goal cushion came via a wonderful 20-yard strike from Nwaneri.
The teenager's Gareth Bale-esque curler also saw him make Arsenal history as the youngest Gunner to score in each of their first two starts for the club, and there was no let-up from Arteta's men once the second 45 got underway.
At the risk of unnecessary injuries, the Arsenal boss sent on some of his big-hitters for the second 45 minutes, although that helped the visitors make their margin of victory more emphatic as Havertz headed home in front of the away end.
To Preston's credit, they continuously attacked their visitors and came close to a consolation a couple of times - Tommy Setford was far from convincing in goal on his full debut - but it was a relatively straightforward evening for Arsenal in the end.
PRESTON VS. ARSENAL HIGHLIGHTS
Gabriel Jesus goal vs. Preston (24th min, Preston 0-1 Arsenal)
A first goal in 25 games for Jesus - how the Brazilian needed that!
Gabriel Martinelli whips in a free kick from the left deep to the back post, where Jakub Kiwior rises above his man to head the ball back into the corridor of uncertainty, and Jesus lashes in a thumping half-volley at Freddie Woodman's near post.
The nine-month drought is over; before tonight, Jesus's last goal came against Nottingham Forest at the end of January.
Ethan Nwaneri goal vs. Preston (33rd min, Preston 0-2 Arsenal)
All aboard the Nwaneri hype train - this kid is something truly special.
Arsenal work it down the right again as Raheem Sterling and Jesus combine before the latter lays off his 17-year-old colleague, who drives inside and picks out the top corner with an astonishing left-footed curling strike from 20 yards.
Oleksandr Zinchenko has his hands on his head, and rightly so. That was beautifully done from the Premier League's youngest-ever player, who is now the youngest-ever Arsenal player to score in both of their first two starts for the club at 17 years and 223 days old - he bagged a brace against Bolton Wanderers in the previous round.
Kai Havertz goal vs. Preston (57th min, Preston 0-3 Arsenal)
Havertz spares Jesus's blushes and then some! Arsenal recycle the ball after Jesus inexplicably tried to head the ball down for a teammate rather than go for goal himself.
Jakub Kiwior sends in a lovely inswinging ball from the left, and Havertz - on as a half-time substitute - gets across his man and fires a bullet header into the far side of the net. 'Kai Havertz scores again' booms out from the away end as the Gunners all but confirm their place in the quarter-finals.
MAN OF THE MATCH - ETHAN NWANERI
Arsenal's 17-year-old wonderkid could not be banging harder on the door for a Premier League start, as he lit up Deepdale with an absolutely fabulous finish from range in the first half, where he was heavily involved in most - if not all - of the visitors' attacks.
The 2007-born starlet came within inches of bagging a second - clipping the crossbar late on - while also misplacing just one of his 55 passes in another performance that will have tongues wagging across North London.
PRESTON VS. ARSENAL MATCH STATS
Possession: Preston 26%-74% Arsenal
Shots: Preston 7-18 Arsenal
Shots on target: Preston 2-10 Arsenal
Corners: Preston 1-7 Arsenal
Fouls: Preston 11-4 Arsenal
BEST STAT
WHAT NEXT?
As Arsenal wait to learn who they will face in the quarter-finals, attention now turns to Saturday's Premier League trip to Newcastle United, while Paul Heckingbottom's Preston endeavour to bounce back at home to Bristol City in the Championship on November 2.