By Isaac Moore at Stonebridge Road
They reached the last eight after a frantic and evenly-fought contest with Charlton and had Josh Vickers to thank for pulling off a string of fine saves in the second half.
The Gunners kept their patience and composure to eventually see off a spirited Addicks side.
Next up for Arsenal - Everton at Emirates Stadium.
SETTING THE SCENE
Carl Laraman made two changes from the side that beat Peterborough in the previous round. Julio Pleguezuelo came in for Stefan O'Connor in the centre of defence while Jack Jebb replaced the injured Daniel Crowley in midfield.
Chuba Akpom took a break from his loan spell at Coventry City to feature in this game and Tuesday's Youth League game against Shakhtar Donetsk.
Arsenal had come through the previous two rounds with relative ease and came into the game as favourites to reach the last eight, but Charlton were not to be taken lightly after their impressive victory over Southampton in the fourth round.
With the backing of a lively crowd at Stonebridge Road, the home side started brightly and had the first effort on goal when Joshua Umerah cut inside Tafari Moore before shooting straight at Vickers.
Arsenal's first chance came after 11 minutes and they should have taken it. Jebb whipped a free-kick towards the back post and Iwobi was unmarked but sent his header over from point-blank range.
In the 25th minute Akpom raced to the byline and cut the ball back to the onrushing Jebb but the midfielder couldn't adjust his feet in time and Charlton eventually cleared.
The best chance of the half came in the 40th minute. Archie Edwards lifted a ball into Karlan Ahearne-Grant's path and the Charlton forward tried to prod an effort past Vickers but the Arsenal stopper was equal to it and pushed the ball away.
Arsenal then immediately broke and Akpom saw an effort tipped wide by Harry Doherty.
The Gunners were better after the restart. Iwobi and Akpom both made sharp bursts into the box but were intercepted before they could get shots away.
In the 57th minute, Jebb unleashed a dipping drive towards the top corner from 25 yards out but Doherty managed to get fingertips to the ball.
Iwobi then had a chance to put Arsenal ahead when he was found by Kamara's clipped cross, but he couldn't generate any power on his header and Doherty made an easy catch.
The game was opening up now. Vickers had to push over an effort from Brandon Hanlan before Charlton missed a glorious chance to go in front.
Arsenal had pushed out but left Umerah onside and free inside the box. A cross came in from the left to the Charlton winger who just had Vickers to beat, but he put his header wide from just three yards out.
Vickers was called into action again with 15 minutes remaining when he made a stunning save to deny Aaron Barnes, who was free at the back post.
Arsenal's goal finally came in the 79th minute. Akpom span past his marker and cut the ball back to Iwobi, who timed his run perfectly and buried his shot into the bottom corner.
Four minutes later, Vickers produced his best save of the night, pushing over Regan Cook's goal-bound effort.
Laraman's team sealed the win in the dying seconds of stoppage time when Tarum Dawkins slid in Maitland-Niles, who rounded Doherty to slot into an empty net.
The young Gunners go marching on.
- Maitland-Niles Goal!
- Zelalem 75
- Jebb 84
- Iwobi Goal!
- Dawkins 75
- Dobson 84
Charlton Athletic Yth
- Harry Doherty
- Levander Pyke
- Regan Cook
- Joe Gomez
- Terrell Thomas
- Archie Edwards
- Karlan Ahearne-Grant
- Joshua Umerah
- Brandon Hanlan
- George Lapslie
- Mikhail Kennedy
- Conor Leon
- Andy Kelly
- Mehawl Martin