Nwaneri shone on a night where Raheem Sterling also opened his Arsenal account, while Declan Rice and Kai Havertz started and ended the scoring respectively for the rampant hosts, whose only blot on the notebook was Aaron Collins's counter-attacking consolation.
With several fresh fitness concerns arising from the weekend's gripping draw with Manchester City, Arsenal boss Mikel Arteta had no option but to throw in four teenage starlets for their full debuts, including 16-year-old goalkeeper Jack Porter and unheralded 18-year-old right-back Joshua Nichols.
Porter entered the Arsenal history books at the youngest player to start a competitive game for the Gunners, and while Bolton did have their moments in the final third in the first half - having a decent early penalty shout waved away - the 2008-born shot-stopper was largely a spectator.
As expected, Arsenal's second-string side dominated proceedings and deservedly went ahead when Rice capitalised on a Scott Arfield error, before three full debutants in Myles Lewis-Skelly, Sterling and Nwaneri combined expertly for the latter's first senior goal.
Nwaneri was at the double early in the second half as Ian Evatt's men played their way into trouble yet again, as the Trotters opted for a high-risk, high-reward approach at the Emirates, which unsurprisingly did not pay dividends when Arsenal were on the ball.
Individual errors did not help Evatt's side either - Nwaneri completed his brace thanks to a schoolboy passing mistake - although the loudest cheer of the night came from the away end when Collins pulled one back after a rapid counter-attack.
However, the 27-year-old's tap-in would not trigger a sensational turnaround, as Sterling restored Arsenal's three-goal lead with his first for the club before Havertz capped off a near-perfect evening for a hotchpotch Gunners team, where the kids were more than all right.
ARSENAL VS. BOLTON HIGHLIGHTS
Declan Rice goal vs. Bolton (16th min, Arsenal 1-0 Bolton)
The Gunners could have given a penalty away in their own box just a few moments ago, but Arteta's men need just one attack to make their quality count, and Rice is off the mark for the new season!
Eighteen-year-old defender Nichols bursts down the right flank and delivers a low cross, which Arfield fails to clear properly, and Rice bends a terrific strike into the bottom corner from inside the D.
Ethan Nwaneri goal vs. Bolton (37th min, Arsenal 2-0 Bolton)
A first Arsenal goal for Nwaneri, who was not even born when the Gunners made the move to the Emirates Stadium in 2006!
It is an exquisite move from the hosts, as Nwaneri's fellow 17-year-old Lewis-Skelly finds the run of Sterling with a defence-splitting pass, and the Chelsea loanee delivers an on-the-money ball across for Nwaneri to bundle home.
Ethan Nwaneri goal vs. Bolton (49th min, Arsenal 3-0 Bolton)
Two for Nwaneri, three for Arsenal, and the Premier League powerhouses are surely cruising into round four.
Bolton defender Chris Forino is the guilty party, playing a lackadaisical pass which Rice is alert to, and the £105m man slots in Nwaneri to score his second of the night under the body of Luke Southwood.
Aaron Collins goal vs. Arsenal (53rd min, Arsenal 3-1 Bolton)
The away end have been in brilliant voice despite their side's chastening evening, and they have their reward just four minutes after Nwaneri completes his brace.
It all comes from an Arsenal corner, as Arteta's men are completely exposed on the break and are powerless to stop John McAtee spraying a delightful pass to his strike partner Collins.
The Trotters striker gives Porter the slip and fires into an empty net from a tight angle to give Evatt's side a sliver of hope.
Raheem Sterling goal vs. Bolton (64th min, Arsenal 4-1 Bolton)
First Nwaneri, now a man nearly 13 years his senior opens his Arsenal account, and Sterling could hardly have wished for an easier first goal in red and white.
Bukayo Saka delays in the right-hand side of the box, and the chance appears to be gone as Bolton regroup, but the 23-year-old produces a brilliant burst of pace to get to the byline and pull the trigger from a tight angle.
Saka's venomous ball across squirms through Southwood's grasp, and Sterling reacts quickest to prod the loose ball into the back of the net from a couple of centimetres out.
Kai Havertz goal vs. Bolton (77th min, Arsenal 5-1 Bolton)
Not long after bagging one of his own, Sterling turns provider - in an unorthodox sense - to set up his former Chelsea teammate Havertz for Arsenal's fifth of the evening.
A special mention for Gabriel Jesus, who nutmegs a Bolton defender before losing a boot, but he still manages to lay off Sterling, who gets a shot away through a few Trotters bodies.
Southwood can only deflect the ball up into the air, and Havertz just gets his toe to the ball before a Bolton defender to prod home into the exposed bottom corner.
MAN OF THE MATCH - DECLAN RICE
Nwaneri's two goals may be the talk of the town, but Rice's £105m quality was just too much for Bolton to handle during his 62 minutes on the field, as the Englishman curled in a delightful opener before being alert to Forino's mistake to set up his teenage colleague.
That assist was one of four chances that Rice created on an evening where he also misplaced just one of his 31 passes and made three interceptions, ensuring that Bolton could not make a game of it against Arsenal's young guns.
ARSENAL VS. BOLTON MATCH STATS
Possession: Arsenal 77%-23% Bolton
Shots: Arsenal 21-4 Bolton
Shots on target: Arsenal 8-1 Bolton
Corners: Arsenal 10-4 Bolton
Fouls: Arsenal 5-8 Bolton
BEST STATS
WHAT NEXT?
Arsenal will learn their fourth-round opponents in a matter of minutes, with the Gunners ball 14 for the imminent draw, but Arteta's attention immediately turns to Saturday's Premier League home clash with Leicester City.
Meanwhile, Bolton - who could take the positives from their display - resume their League One promotion push away to Crawley Town on Saturday lunchtime.