A Mark Revins goal after 68 minutes was enough to earn Drogheda a precious three points and assure the Boynesiders of Premier Division football next season.
Visiting goalkeeper Josh Moran will have to shoulder part of the blame for a defeat which virtually ends Kilkenny's outside hopes of going up, when he allowed himself to be beaten at the near post by Revins's shot from just inside the box.
Revins and goalkeeper Gareth Byrne, who had been serving three match bans were cleared to play just 90 minutes before kick-off when their suspensions were cut from three games to two following a successful independent arbitration hearing.
Drogheda Utd: Byrne, Murphy, Boyle, Impey, Maher, Coleman, Beggs, Fox, Revins, O'Dowd, Thornton.
Kilkenny City: Moran, Arrigan, Carolan, R Walsh, D Walsh, Jordan, Cashin, P Walsh, Vaughan, Kelly, Rea. Sub: Goodwin for P Walsh.
Referee: D Hancock (Dublin).