The German completed 57 minutes at the Emirates Stadium, where Paul Harsley’s side twice fought back from a goal down, before taking control of the game late on to seal all three points.
Folarin Balogun scored either side of Adrian Bernabe’s strike to put the hosts 2-1 up on the hour mark, but a sublime solo goal from Jayden Braaf put City in the driving seat after Taylor Harwood-Bellis had bundled home an equaliser.
Bernabe netted his second to ease the nerves and wrap up the points in the dying minutes.
It was a nightmare start for City, who fell behind inside two minutes when Arsenal's top scorer, Balogun, turned smartly in the area and drove an unstoppable shot into the roof of the net.
Braaf might have equalised within minutes after he beat Ainsley Maitland-Niles with a drop of the shoulder, but goalkeeper Matt Macey was equal to his fierce strike.
The first period belonged to the hosts, with Rowan McDonald forced to make a saving tackle as Balogun bore down on goal, before Ben Cottrell curled a glorious chance wide of Gavin Bazunu’s post when he had time and space to pick his spot.
City, having struggled to create, drew level in fortuitous circumstances.
Arsenal cleared a corner only as far as Bernabe, whose 20-yard effort cracked against the foot of the post, only to rebound off Macey’s back and into the net.
Sane’s comeback ended on the hour mark, when he was replaced by 17-year-old Liam Delap and, as in the first half, it was the Gunners who started the brighter after the break.
Balogun grabbed his second when he coolly slotted past Bazunu after his pace took him clear of the City defence, who were left relieved when Trae Coyle rounded the visiting keeper only to see his effort cleared off the line.
The sense of relief was heightened when Harwood-Bellis tapped home an equaliser from close range and from there we played our best football.
It was personified by Braaf’s brilliance, cutting in off the right the Dutchman turned the retreating defender inside out before sliding it inside Macey’s near post.
And, with the final whistle approaching, Bernabe confirmed a deserved victory when he reacted quickest to poke home a fourth.
Step forward for sane
The 24-year-old’s involvement in North London was a huge boost for both the player and Pep Guardiola, as he took the next step in his recovery.
Often hugging the left touchline, with occasional runs inside, it was a steady return in which he felt his way back into the matchday environment.
By his own admission, he has a way to go before he is back to his best, which you would expect after a six month absence, but he still showed flashes of quality against the Gunners.
He started the move for Braaf’s early chance, coming in off the left flank and switching the play, whilst he may have claimed an assist had Cole Palmer not strayed offside to collect his slide rule, defence splitting pass.
All in all, it was a positive step forward for the winger.
How we lined up
Harsley made three changes to the side that lost to Brighton and Hove Albion two weeks ago, with Harwood-Bellis and Cole Palmer coming in alongside Sane.
Bazunu’s goal was protected by a back four of Alpha Diounkou, McDonald, Harwood-Bellis and Nat Ogbeta.
The midfield three was unchanged, with Tommy Doyle sitting deepest and Bernabe and Felix Nmecha just ahead of him, whilst Sane operated on the left flank and Braaf on the right, with Palmer playing through the middle of the forward line.
What it means
Our sixth league win of the season moves us up to eighth in the Premier League 2 table, with 21 points from 18 games.
The EDS embark on a two week break now, returning with an away trip to Leicester City on Monday 16 March with kick-off at 19:00 (UK).
However, several of the players involved in this game will be part of the U18s squad for the FA Youth Cup quarter-final against Burnley on Wednesday 4 March.
Kick-off is at 19:00 (UK) at the Academy Stadium and you can also watch the game live on CITY+.