However, Danny Allsopp was pushed over in the box midway through the half, and Stuart Green put the penalty in the bottom corner beyond goalkeeper Paul Sharp's reach.
Just before half time, Green set up Nick Barmby to put City in front. Barmby was on the end of his through ball and he dinked a shot over Sharp which the covering defender couldn't prevent going in.
Two of the half time substitutes linked up for the third. Jon Walters crossed from the right, and Stuart Elliott powered a header home.
Aaron Wilbraham hit the crossbar, but got his name on the scoresheet soon after with a header.
Ferriby got a consolation when Marc Joseph overhit a backpass into his own goal, so it finished 4-2 and City took home the trophy for a second year running.
City line-up (4-4-2): Myhill; Thelwell (Donaldson 60), Joseph, Delaney (Hinds 45), Dawson (Wiseman 52); France (Butler 65), Ashbee (Walters 45), Lewis, Green (Elliott 45); Allsopp (Wilbraham 45), Barmby (Fry 54).