Nick Cushing’s side, who had opened the scoring through Natasha Flint’s stunning long-range effort, surrendered their lead just after the hour-mark before conceding again in the final minute of normal time to gift the hosts a valuable three points.
The victory lifts Chelsea up to second in the FA Women’s Super League table, five points clear of the Mancunian outfit.
City headed into the clash on the back of seven wins in their last eight games and in the knowledge they needed another one to keep their title hopes alive.
With that in mind, Cushing named an unchanged side from the one that secured a 1-0 win over Notts County on Thursday night. New signing Emma Kete was named on the bench.
The visitors made a bright start with Krystle Johnston firing two efforts towards goal inside the opening ten minutes. The first curled wide but Chelsea goalkeeper Marie Hourihan had to be alert to keep out the second.
Hourihan was called into action again shortly afterwards, producing a fantastic save to claw away a Toni Duggan effort.
A minute later, it was Karen Bardsley’s turn to keep the scores level, tipping over a long-range shot. From the resulting corner, Katie Chapman headed over.
Johnston then tried her luck once more from distance. The strike looked to have been pushed over but instead a goal-kick was awarded.
Eniola Aluko tested Bardsley again on 24 minutes, as the striker began to create more and more for the home side, using her lightning pace to run at the City defence. She would cause problems for the visitors all afternoon, ghosting past players with ease before delivering a number of dangerous crosses into the area.
It was the away side who broke the deadlock though with a fine piece of individual skill of their own.
Just as she did against Notts County, Flint picked up the ball in the opposition half and ran at the defence. This time though, she spotted Hourihan off her line and planted a glorious lob over the goalkeeper that dipped into the back of the net.
It was the youngster’s third of the season and second in two games – proof that despite her age, she can compete at the highest level.
Chelsea responded well to going behind and would have equalised within three minutes if not for Bardsley.
City’s afternoon took a turn for the worse just before half-time, when captain Steph Houghton went down with what looked to be a serious head injury. Fortunately, though it had looked to be the case, the stretcher was not required. The skipper did require stitches though will be monitored over the next few days.
When play continued, Bardsley was on hand to make yet another stop and the Blues hung on for a half-time lead.
After the break, City pressed for a second. Duggan’s effort flew off-target before the visitors were given a huge let-off, when Yuki Ogimi somehow fired over at the back-post from close-range.
Isobel Christiansen then curled a shot straight at Hourihan, after winning the ball back well, but as Chelsea pressed, City’s resilience was broken on 61 minutes, when Chapman headed an equaliser into the bottom corner.
With the scores back level, both sides sought a winner. Jill Scott and Rachel Williams both headed off-target before Bardsley produced two more fine saves.
As the game entered its final minutes and with Chelsea in the ascendancy, City were hanging on somewhat and were dealt the killer blow in the dying seconds as substitute Jackie Groenen stole possession from Betsy Hassett before playing a one-two, rounding Bardsley and slotting the ball into the back of the net to give the home side the win.
Next up, MCWFC host Liverpool Ladies in another crucial league encounter on Sunday 27 July. Ticket details will be released in the next few days.