Two goals in three first-half minutes from the hosts gave City a mountain to climb after the break but Adam Drury halved the arrears a minute into the second period.
An incredible point-blank save from Arsenal keeper Matthew Macey prevented Devante Cole from equalising after 56 minutes, before Stefan O’Connor scored a decisive third goal to restore the two-goal advantage, 20 minutes from time.
In the dying embers, second half substitute Cole scored and Arsenal’s Ajayi turned the ball into his own net on either side of Jon Toral’s second strike to set up a grandstand finale but the home side held out for all three points.
Boreham Wood’s Meadow Park was the venue for this Monday night clash which gave the Blues an opportunity to strengthen their bid for a place in the four-team u21 Premier League finals, while Arsenal still harboured ambitions of a top half finish.
Patrick Vieira’s side still had four games to make up on two of the four teams above them but knew a win could move them up as high as third, depending on results elsewhere.
Fulham and Southampton have both completed their regular season calendars, so would have been hoping to see City slip up in North London to maintain their places in second and third respectively.
With a Barclays u21 Premier League cup final first leg against Reading coming up at the Etihad on Thursday night, Vieira made four changes to his side for his first return to Arsenal as a manager.
Angelino, Drury, Jason Denayer and Marcos Lopes all came back into the side after the semi-final win over Burnley last week.
Three of the jewels of the Gunners’ prolific academy were rested, namely Dan Crowley, Gedion Zelalem and Chuba Akpom ahead of their FA Youth Cup semi-final against Chelsea on Thursday.
City have made blistering starts to their last three games, opening the scoring inside the first ten minutes on each occasion but this time it was the hosts who almost grabbed an early advantage.
Jon Tornal embarked on a mazy dribble and tested Ian Lawlor with a good strike but the Irishman made the save and Thomas Eisfeld sent the subsequent rebound wide of the target.
Although the Gunners enjoyed some pressure on the City goal in the opening ten minutes, Shay Facey and Jason Denayer were solid and successfully limited the threats posed by Jack Jebb, Isaac Hayden, Toral and Hector Bellerin.
The Blues, playing in all-black, hit their stride a quarter of an hour into the game and began to wrestle control of the match.
Lopes saw his half-volley drift wide of the target, before Seko Fofana struck a 25-yard shot which forced Matthew Macey into a parried save after 17 minutes.
A minute later, Sinan Bytyqi hit an excellent free-kick which drew the best out of the Arsenal goalkeeper again.
However, it was Arsenal who took the lead with ten minutes to go in the first period.
Eisfeld was tackled four yards from goal and the ball ricocheted favourably for Toral to tap home the opening goal.
Three minutes later, the advantage was doubled and the Blues had it all to do after Bellerin ran through on goal and slotted the ball underneath the onrushing Lawlor.
City haven’t been two behind at any stage in a game since February’s 3-2 comeback win over Newcastle.
A similar reaction was required to prevent a sixth defeat of the campaign and they got off to the perfect start on that score, halving their arrears almost immediately after the restart.
Right-back Drury has spoken of his desire to add goals to his repertoire in recent weeks and he got his second of the season after 46 minutes, driving the ball past Macey from the edge of the area to make it 2-1.
That goal prompted a surge of belief in the City ranks and it was Arsenal who were being forced to play the game facing their own goal in an attempt to stem this tide of Blues pressure.
The pivotal moment in the match arrived after 56 minutes when an incredible save from the Arsenal keeper prevented Cole from levelling after the City forward got on the end of a Lopes cross.
The 18-year old spread himself to block the England youth international’s shot from point-blank range – a save which would carry huge significance at the end of the night.
Vieira’s men kept piling forward in an entertaining second half but, in doing so, inevitably left gaps to be exploited on the counter-attack which the Gunners nearly profited from with a couple of presentable chances but Eisfeld and Olsson squandered their opportunities.
Eventually, Arsenal did manage to capitalise on the away side’s forward thrusts when O’Connor looked to have put the game beyond doubt, slotting home at the second time of asking after 73 minutes.
However, the game burst to life again with the final whistle approaching with three goals in four minutes.
First, Cole converted a Bytyqi cross after 89 minutes before Toral went up the other end and scored his second goal of the game.
The entertainment wasn’t over there as Arsenal defender Ajayi glanced a corner into his own net to briefly ignite hopes of an unlikely comeback but they were quickly extinguished by the full-time whistle.
City will take heart from the fact that they never gave up and will hope to take out their frustrations on Reading in their cup final on Thursday.
Seasoncard holders can attend for free and ticket details can be found here.
