Fran Kirby’s strike in injury time of extra time booked the holders’ place in the FA Cup final at the national stadium, after Ji So Yun had cancelled out Jane Ross’ effort late on in normal time.
The result saw Nick Cushing’s side fall at the semi-final stage to the Londoners for the second successive season, though again the result was harsh on the visitors.
In a cagey affair which saw plenty of tackles fly in, City battled valiantly. Neither side secured a foothold in the game but there were spells of pressure for both sides.
The Blues’ boss opted to field the same starting XI which defeated Arsenal, as Karen Bardsley, Jill Scott and Toni Duggan were recalled. Marie Hourihan returned to her old stomping ground and took her place on the bench, alongside the fit-again Jennifer Beattie.
City’s first chance of the afternoon fell to Abbie McManus, who collected the ball on the edge of the area and fired just wide. Steph Houghton then struck a free-kick which looked destined for the top corner but was clawed away well by Hedvig Lindahl.
At the other end, Chelsea were restricted to long-range attempts.
The second half mirrored the first with the away side creating the better of the chances.
Nikita Parris unleashed a powerful shot just over the bar, having been played through by Scott, while Duggan went close with a hooked effort which hit the sidenetting.
The deadlock was broken on 72 minutes with a goal as scrappy as the game itself. A corner sparked pinball in the box and the ball fell kindly to Ross, who poked home.
It arrived a little out of the blue but City didn’t care.
The hosts responded well to falling behind though and manager Emma Hayes opted to make changes in a bid to level the score, bringing on Drew Spence and Kirby.
Chelsea piled pressure on the visitors’ defence and found an equaliser with five minutes of normal time remaining as So Yun - City’s nemesis in the semi at Wycombe last season - curled into the bottom corner.
Having clawed themselves back into the game and with a vocal support behind them, the home side rode their momentum. Eni Aluko should have given her side the lead but slid straight at Bardsley, while Gemma Davison drilled inches wide.
Scott went close for City, as her header was saved on the line by Lindahl - and the Blues were dealt the suckerpunch with seconds remaining as Kirby ghosted through the defence and fired home.
It was very cruel on the away side, who had fought for everything throughout and deserved to at least take the tie to penalties.
The other semi saw Arsenal thrash Sunderland 7-0, and the two London clubs will meet on Saturday 14 May.
Next up for City, it’s Birmingham away in the WSL on Sunday 24 April. Kick-off is at 2pm.