Erin Doran rescued a point for Llandudno with an equaliser direct from a corner five minutes into added time at the Essity Stadium.
It looked as though Flint had clinched the win when Kaelyn Williams made it 3-2 with an absolute screamer in the 89th minute, but the deposed champions battled to the end and gained a late reward.
The Silkwomen got off to a flyer, Llinos Hughes heading them in front after seven minutes from a Rosie Hughes free kick.
A minute later it was 2-0. Rosie Hughes fed a ball to the flank, from where Ruby Hastings sent in a cross for Zoe Stopford, who took a touch and fired in number two
Llandudno rallied and cut the deficit on 16 minutes when Kelsey Davies notched her 15th goal of the season.
And it was all-square after 32, Jasmin Dutton providing the assist for Angharad Jones to level matters.
The majority of the second half was goalless, with Llandudno’s young keeper Beca Davies producing some great stops, especially in one-on-one situations.
The game was heading for a draw when Kaelyn Williams lashed home a stunner from outside the box with just a minute of the 90 left.
Flint may have thought they had it won, but Doran’s well-flighted right-foot corner with 95 on the clock ensured it finished honours even.
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