Red Rewind: Battling City overcome the odds
The Minstermen were notably without key forward duo Jon McCarthy and Paul Barnes, while Glenn Naylor and Graeme Murty also missed out having both started the midweek 4-1 victory against Leyton Orient.
Into the side for a senior debut came 21-year-old Middlesbrough-born striker Nicky Peverell, with Scott Jordan and Wayne Hall also recalled into midfield by manager Alan Little, himself a pitchside flu-victim.
Their opponents included towering ex-City striker Ian Helliwell, although it was his forward partner Alun Armstrong who immediately slotted in the opener after Dean Kiely had initially blocked.
But York, who had lost the reverse meeting 4-2 earlier in the season and were indebted to goalkeeper Kiely on a number of occasions this time, replied with a couple of goals prior to the interval.
Firstly ex-Hartlepool United centre-forward Paul Baker, a £15,000 buy from Gillingham the previous October, deceived keeper Neil Edwards at his near post from just inside the area.
And just five minutes later midfielder Nigel Pepper jinked beyond an opponent and drove low into the far corner to establish the visitors a lead.
County were to draw level, though, with only three minutes of the contest remaining as Jim Gannon turned six-yards out after a long throw was helped on.
However, York went straight back to the other end, where Baker's header was diverted past replacement keeper Matt Dickens by home centre-back Tony Dinning following Hall's free-kick.
Stockport County: Edwards (Dickens 46), Connelly (Chalk 46), Todd, Ware, Flynn, Dinning, Gannon, Wallace, Helliwell, Armstrong, Beaumont
subs (unused): Graham
Goals Armstrong (5), Gannon (87)
York City: Kiely, McMillan, Wilson, Pepper, Tutill, Atkin, Peverell, Jordan (Barratt 62), Baker, Hall, Canham
subs (unused): Cresswell, Warrington
Goals: Baker (38), Pepper (43), Dinning OG (88)
Ref: J. Watson (Whitley Bay)
Video Link: YorkCityTV