United's return to league action following cup exploits was ruined by two late goals in Kent.
On the day that Gillingham announced Justin Edinburgh as their new manager, Jermaine McGlashan and Cody McDonald netted the late strikes to give the home side victory.
Jason Holt made his debut from the bench but there was no place for new striker Matt Done, who is nursing a minor injury.
Following the disappointment of the midweek FA Cup defeat, chief Clough rung the changes again - five in total. Brayford, Davies, Adams, Reed and Coutts started and McEveley was named as captain.
Davies was involved in the game's first talking point, being accused of handball in the penalty area but referee Williamson was unmoved, whilst United's first chance came as the result of mistakes in the home defence but Gillingham cleaned up after goalkeeper Nelson dropped Ehmer's sliced clearance.
After the initial exchanges United looked good on the break and won a couple of corners, from one of which, Gillingham were forced to clear off the line twice from a Davies delivery, the first from one of their own defenders and the second from Brayford.
On 21 minutes, Nelson tipped away an Adams shot after Davies laid off following Murphy's run and Gillingham hit back with a Dack free-kick, which struck the wall after McEveley's foul on McDonald.
The limited chances were coming at both ends. Reed's impressive control, turn and shot brought a good save out of Nelson, who held on when Murphy was lurking and Gillingham's McDonald chipped onto the roof of the net after being gifted possession by Baxter.
The final chance of the half did fall to the Blades and Adams looked as though he was struggling to keep possession but he managed to evade three defenders before half-volleying over the crossbar.
After the interval the contest was open in early exchanges with both outfits trying to utilise space. Coutts cut in from the right but shot over and Gillingham went mightily close on 56 minutes when McDonald volleyed Hessenthaler's cross against the bar from 18 yards.
Just after the hour Campbell-Ryce replaced Davies and as Gillingham looked to boss the midfield at the midway stage of the half, Dack clipped wide from Hoyte's pull-back.
Holt was given his debut for the final 15 minutes, replacing Baxter, but the next chance fell to Murphy following a run from the left but his effort was held by Nelson.
McNulty was thrown on in the final ten minutes, taking over from Adams, but disaster was moments away. A United punt out of defence was countered by similar from Ehmer, however, his clearance dropped behind McEveley and perfectly for McGLASHAN, who just poked beyond the onrushing Howard and into the empty net.
Late on Basham was thrown forward as an emergency, extra striker and McNulty battled with Egan to try to capitalise on a mistake but the only late goal came on the break at the other end. Reed gave away possession and McGlashan's pace allowed McDONALD space and he lashed home from the edge of the box - the final action of the fixture.
Gills: Nelson, Garmston, Egan, Ehmer, Loft, Hessenthaler, Marquis (McGlashan 79), McDonald, Pritchard (Galbraith 45), Dack, Hoyte.
Unused: Legge, Morris, German, Norris, Dickenson.
Blades: Howard, Harris, Brayford, Basham, Murphy, Baxter (Holt 76), Davies (Campbell-Ryce 63), Coutts, McEveley, Reed, Adams (McNulty 84).
Unused: Doyle, Turner, Freeman, Kennedy.