Claire Emslie had given City the lead midway through the first half before a Liverpool penalty early in the second left Nick Cushing’s side fighting for the winner.
In dramatic style, Beattie rose to meet Caroline Weir’s excellent free-kick three minutes into injury time to secure an all important triumph for the Blues.
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The victory sees City keep the pressure on league leaders Arsenal who secured a 1-0 away victory earlier in the day over Birmingham City.
And, crucially, it also confirmed the Blues place in next season's Champions League with Chelsea having only been able to draw with West Ham earlier, ensuring at least a top-two finish for Nick Cushing's side.
Before kick-off, a minute's silence was held in honour of Manchester City Life President Bernard Halford, who sadly passed away earlier in the week. City players also all sported black armbands in his memory.
After a cagey opening 25 minutes the first real chance of the game fell to Abbie McManus after a sublime set-piece ball into the box from Caroline Weir found the right-back, who could only strike the ball over the bar.
However, just moments later and the ball did find the back of the net. Claire Emslie struck a low ball from the edge of the box into the bottom left-hand corner of the goal and fired City into the lead.
Nick Cushing's side really began to ramp up the pressure and just a minute later it was nearly two. Captain Steph Houghton fired a superb shot from the edge of the box against the cross-bar before Parris’ follow-up come back off the post.
After going into the break with a 1-0 lead, Liverpool made it level shortly after play resumed. A scramble in the box saw the visitors handed a penalty for handball, one which Courtney Sweetman-Kirk slotted into the bottom right corner, with City keeper Ellie Roebuck unfortunate not to keep it out after getting a hand to it.
City had several chances in the final 20 minutes to seal the victory with chances falling to Weir, Parris, Demi Stokes and substitute Georgia Stanway but Preuss was in fine form between the posts for Liverpool.
Finally however, City secured a much-deserved victory as Beattie headed home with what was almost the last touch of the game to keep the pressure on title rivals and league leaders Arsenal.
How we lined up
Roebuck started between the sticks for City, shielded by a back four of Stoke, Beattie, Houghton and McManus.
Walsh and Scott sat in holding midfield for the Blues with Weir and Emslie in attacking midfield and a front two of Parris and Hemp.
With no game for two weeks, City’s next fixture comes against Chelsea in the semi-final of the FA Women’s Cup on Sunday 14 April. With City drawn as the home side, the game will be played at the Academy Stadium with kick-off scheduled for 3:30pm BST.