The final started cautiously before the Citizens broke the deadlock through a brilliant free-kick from Floyd Samba, whose curling effort flew into the top corner.
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United responded just 59 seconds later when Godwill Kukonki punished a defensive error to head home the equaliser.
Both sides pushed for a winner in a fiercely contested Manchester derby, with City creating the better chances after the break.
Heskey twice threatened before finally delivering the decisive moment late on, arriving inside the box to convert Ryan McAidoo’s cross and secure City’s fifth FA Youth Cup title.