Harps started in bright fashion and took the lead after just five minutes of play when player-manager Anthony Gorman acrobatically finished off a right wing cross from Shaun McGowan.
The visitors will feel that they could have doubled the advantage on 18 minutes when Barry Curran and Stephen O'Donnell were both denied by Kilkenny 'keeper Stephen Cashen.
The all important second goal arrived after 29minutes and it was well waiting for with Gary Crossan striking a sweet right-footed volley past the 'keeper after an excellent cross from Barry Curran.
It was a fine way for the Killea man to cap his return to the side with the only disappointment being that there was little more than 50 spectators in attendance to witness what was a sublime goal.
The hosts will feel that they should have pulled one back before the interval as James Gallagher's crossbar twice came to Harps' rescue. Twice Kilkenny midfielder Conor Buckley found himself in space on the edge of the six yard box but on both occasions he struck the upright.
The second half saw the game die out with little or nothing in the way of goalmouth incident in part two.
The only chance warranting entry into the notebook was an 81st minute effort from Willie Doyle which was dealt with by James Gallagher.
Davitt Walsh made a return to the Harps side for the final 10 minutes, but Stephen O'Donnell, whom he replaced, limped off what looked to be an ankle injury while another positive was the appearance late on of young James Doherty.
Doherty is the latest in the ever-growing crop of youthful talent to progress to the first team as he made his competitive debut coming on as an 81st minute replacement for Barry Curran.
Harps now welcome league leaders Galway United to Finn Park next Saturday night next in what will be a tricky tie for the Ballybofey brigade with the Tribesmen expected to bring a sizeable travelling support with them.
Kilkenny City: Stephen Cashen; Conor McMahon, Cathal Sweetman, Aaron Mooney, Sean L'estrange; Paul Donnelly, Conor Buckley, Brian King, Peter Higgins; John Brophy, Willie Doyle. Subs: Barry Lennon and Graham Mulvey (for Donnelly and L'estrange, 67mins).
Finn Harps: James Gallagher; Shaun McGowan, Jonathan Minnock, Eloka Asokhu, Matthew Crossan; Michael Funston, Barry Curran, Anthony Gorman, Shane O'Connor; Stephen O'Donnell, Gary Crossan. Subs: David Bell (for G.Crossan 72mins); Davitt Walsh (for O'Donnell); James Doherty (for Curran, 81mins)
Referee: Conor Fitzgerald.
Finn Harps Dot Com Man-of-the-Match: Harps had a number of notable performers this evening with Jonathan Minnock performing admirably at centre back and Michael Funston and Anthony Gorman pulling the strings to perfection in the middle of the park.
However, the man of the match this evening goes to a man who was so out of favour some weeks back that he was on the verge of signing for Institute. Gary Crossan came back with a bang tonight, capping a fine evening at the office with a cracking goal on 29minutes to put his side two in front.