United's miserable recent home record continued, despite pushing MK Dons back for much of this re-arranged encounter.
MK Dons picked up a total of seven bookings in trying to contain the Blades but the visitors won it with a late goal, Dele Alli scoring after Mark Howard kept out Danny Green's free-kick.
The Unitedites vented their displeasure at a number of decisions made by the match officials at the final whistle.
One of the two of Clough's changes was O'Grady, who was handed his Blades debut from the start. Flynn was also included and started at right-back, allowing Basham to play in midfield. Baxter and Higdon dropped to the bench.
The early possession was dominated by the visiting side but all they had to show for the opening 15 minutes was a weak Spence header at Howard, whilst McEveley stopped Alli's run. The home side's early endeavours saw a side-foot from Basham saved and Scougall sliced wide following a corner routine.
On 20 minutes a neat Blades move from right to left saw Doyle's pass allow Harris to deliver across the box but Basham was unable to connect and there was further bad news three minutes later when O'Grady limped off - McNulty was the replacement.
Campbell-Ryce shot at Martin from an acute angle and McCarthy headed over after a flap from the visiting goalkeeper from a corner as the Blades looked to get on top. A number of strange decisions from the officials upset both sides and Hodson and Alli were the recipients of yellow cards just before the break.
United made the brighter start to the second half with Campbell-Ryce prominent. He delivered the cross which Scougall could not convert and then the Scottish midfielder shot wide on 50 minutes.
McEveley was booked for kicking the ball away but United's attacking intent continued. McNulty shot wide following a corner and Campbell-Ryce's cross arrived with too much pace for Basham.
The visiting side's first opportunity of the second period arrived on 62 minutes but Kay's low header from Baker's corner as kicked away by Murphy, who then shot at Martin from a narrow angle moments later.
On 76 minutes United had the ball in the net but the officials stepped into before the celebrations could start. From a Harris free-kick, Basham won the initial header, which hit a post, and McCarthy followed up to put the ball in the net but a linesman's flag adjudged the Blades to be offside.
Baxter replaced Scougall for the last ten minutes, followed by McGahey taking over from Basham, but disaster was just around the corner. McEveley's foul on Kay gave Dons a free-kick 20 yards out and although Howard did tremendously to keep out Green's powerful effort, ALLI followed up to score.
From a free-kick, McCarthy's header rested on the top of the goal and McNulty turned a Flynn cross goalwards but Martin saved comfortably. Five minutes of added time saw United on the attack but Doyle's first-timer was blocked and the visitors repelled a couple of corners to secure their victory. The last action was Green sent off for two bookable offences, both slowing down the play.
Blades: Howard, Harris, Basham (McGahey 86), Flynn, Doyle, Murphy, Scougall (Baxter 81), McEveley, Campbell-Ryce, McCarthy, O'Grady (McNulty 23).
Unused: McGahey, Higdon, Reed, Turner, Adams.
MK Dons: Martin, Hodson, McFadzean, Kay, Potter, Reeves (Abofe 55), Grigg (Flanagan 90), Spence, Baker, Alli, Powell.
Unused: Green, Bowditch, McLoughlin, Baldock.