Two second half goals condemned the Blades to defeat on the final Saturday before the Sky Bet Football League kicks off.
Unitedites filled more than half of the Bootham Crescent crowd (992 of 1,761) but Ryan Jarvis netted both of the goals that secured York City's victory.
Wearing the new black away shirts for the first time, United saw a lot of the ball in the opening ten minutes with some neat passing in the middle third. However, the first chance was gifted to York following a mistake by ex-Blackpool duo Basham and McGahey but Coulson side-footed wide.
The next chance was also York's but Howard made an important reaction save to deny Lowe from Penn's free-kick and Baxter, a minute before being replaced by De Girolamo, clipped United's first chance just wide after a mistake in the home defence.
Just after the half hour Basham's glancing header from Alcock's cross trickled wide whilst boss Clough was forced into a second change on 38 minutes when Dimaio took over from Wallace and the spell immediately before the break was similar to kick-off when United controlled possession without troubling goalkeeper Ingham.
United made another change at the break, McNulty taking over from Alcock, but a succession of corners for the home side paved the way for them to take the lead on 56 minutes. Howard had already claimed a number of Meikle's deliveries but on this occasion there was a spell of pinball before JARVIS forced the ball into the top corner.
The Blades responded with efforts from Dimaio and De Girolamo and then McNulty appeared to be tripped by McCombe but referee Eltringham refused any penalty claims.
Clough was readying further changes when York added a second on 69 minutes. With United's defence overstretched, JARVIS linked up with Meikle before slotting past the exposed Howard.
On 72 minutes, Butler, Doyle, McGinn and Porter were all introduced as United looked to get back into the game. Harris almost put McGinn in the clear and the latter came close to doing likewise for McNulty.
Butler twice went close from set-pieces late on but it was not enough to prevent the Blades slipping to a third defeat of the pre-season campaign.
York: Ingham, McCoy, Coulson, Penn, Jarvis, Straker, Lowe, Winfield, Platt, Meikle, Murray.
Subs: Mooney, McCombe, Parslow, Montrose, Hirst, Rzonca.
Blades: Howard, Alcock (McNulty 45), Harris, Wallace (Dimaio 38), Basham (Doyle 72, Flynn, Murphy (Porter 72), Scougall (McGinn 72), Baxter (De Girolamo 24), Collins, McGahey (Butler 72).