Pauline Bremer tapped home the opener on the stroke of half-time after an evenly balanced first 45, before Lauren Hemp headed us two ahead within five minutes of the restart following a typically inch-perfect cross from Keira Walsh.
Danielle Van de Donk gave the visitors hope after she reacted quickest to a reaction save from Ellie Roebuck, but Nick Cushing’s side held on to move three points clear of the Gunners and become outright leaders of the Women’s Super League.
It was just rewards for the boss, with the entire team fighting until the end to make sure he capped off an incredible six years at the club with a win before his move to New York City.
Both sides seemed willing to get the measure of each other in the opening stages, but City almost found the breakthrough in the first five minutes.
A clever corner routine saw Caroline Weir drill in a low ball to the edge of the penalty box, but the onrushing Georgia Stanway couldn’t make a clean enough contact to guide her effort on target.
That chance seemed to spring the away side into life, with Walsh's timely block taking the sting out of Beth Mead’s volley towards goal in a dangerous area.
City were in need of some inspiration, and they almost found it when Stanway’s defence-splitting pass found Jill Scott, but the midfielder’s cutback fell agonisingly short of Ellen White’s left boot.
However, the breakthrough finally came in the 44th minute.
Weir’s free-kick from the right caused havoc in the Arsenal defence and, after a bit of penalty box pinball, Bremer was in the right place at the right time to guide home her 10th goal of the season from within six yards.
The best possible end to the half for City, and it got even better after the restart...
The second followed soon after the break, when Walsh’s inviting cross from the right found an unmarked Hemp at the back post.
The winger opted for a first-time header rather than to bring the ball down and it proved to be the right decision as her header looped in expertly off the crossbar to double our lead.
City were beginning to build some momentum and looked dangerous every time they came forward, but Arsenal continued to offer a threat at the other end, and had soon halved the deficit.
Jordan Nobbs’ close-range effort forced an incredible save from Ellie Roebuck down to her right, but our goalkeeper could do nothing to prevent Van de Donk from poking the visitors back into the game just before the hour mark.
Ten minutes later and it was almost a similar story with Van de Donk stealing in at the far post, but this time it was a combination of Demi Stokes and Roebuck who came out on top, somehow guiding the ball out for a corner.
And from that set-piece our number one had to be on hand once again to preserve our slender advantage, parrying away a vicious effort across goal from an unmarked Vivianne Miedema.
With the game hanging in the balance going into the final ten minutes, Arsenal continued to press for an equaliser, but the defence held firm and saw out a deserved win.
“There’s only one Nick Cushing” rang around the Academy Stadium as the game drew to a close, and he will be extremely proud with how his team ground out the win in his final game at the helm.
How we lined up
Roebuck started between the sticks, screened by a back four of Stokes, Gemma Bonner, Steph Houghton and Stanway.
Walsh and Weir sat in front with Jill Scott and Hemp on the flanks.
Ellen White and Bremer started at the sharp end of the team as a front two.
What it means
The win sees us move three points clear of the Gunners as we lead the Super League outright. Chelsea's emphatic home win over West Ham means they move up to second, one point behind us with a game in hand.