In another even game at the top of League One, United suffered a first defeat of 2015.
It was a tale of one good chance for each team.
Jamal Campbell-Ryce's effort hit goalkeeper David Martin's leg and trickled just wide, whilst for the MK Dons, Carl Baker slotted home midway through the second half.
After the previous week's victory over Preston, boss Clough made just one change with Alcock taking over at right-back from Flynn. On the bench, Long replaced Turner as the back-up goalkeeper.
A tentative start by both sides saw limited opportunities in the early exchanges. A Carruthers shot deflected off both Kennedy and Baxter but dropped nicely for Howard and two pieces of skill from Baker enabled him to get a shot away but he sliced wide.
Campbell-Ryce was attempting to run at Lewington at every opportunity but United's only chance of the opening half hour was a long-range Doyle shot, which was deflected wide.
Later in the half, chances began to materialise. Baker shot over on the turn and then tried his luck again after linking up with Grigg but Howard pushed the ball around a post.
For United, who had Baxter and Harris booked, Kennedy looked to be impeded as he attempted to meet a Baxter free-kick but the best chance of the whole half saw the Dons defence caught out by a quick Harris free-kick on 44 minutes but Campbell-Ryce's effort, in a one-on-one situation with the goalkeeper, hit the inside of Martin's leg and trickled just wide.
The Blades made a change at half-time with Reed taking over from Scougall and the teenager was quickly into the thick of the action. The first effort after the break saw Howard save from Spence before Baxter and Harris did particularly well to keep possession ahead of Reed striking just wide from 20 yards.
Both managers made alterations to their forward lines with Higdon replacing McNulty but the home side opened the scoring with their next attack. Passes from Lewington and Grigg opened up space for BAKER, who sidefooted past Howard from just inside the box.
United's responses surrounded Campbell-Ryce's deliveries from the right. His first found Murphy but there was not enough pace to beat Martin and second saw McEveley get a flick but the ball rolled agonisingly wide on 75 minutes.
Predictably, the pressure late on came from the visitors, although Martin was well protected. Adams replaced Alcock in an attacking move and the substitute fired a free-kick on target on 84 minutes but the effort was at the home goalkeeper.
Four minutes of injury-time was announced but Higdon could not repeat his heroics of the Capital One Cup tie, heading wide a Baxter free-kick late on, whilst the final chance was a half-volley from Doyle, which was wide.
MK Dons: Martin, Lewington, McFadzean, Kay, Bowditch (Clarke-Harris 65), Reeves (Baldock 90), Grigg, Spence, Baker, Alli, Carruthers (Randall 86).
Unused: McLoughlin, Hodson, Green, Hitchcock.
Blades: Howard, Alcock (Adams 82), Harris, Doyle, Murphy, Scougall (Reed 45), Baxter, McNulty (Higdon 65), McEveley, Campbell-Ryce, Kennedy.
Unused: McGahey, Long, Dimaio, K. Wallace.