Two late goals from Michael Higdon ensured the Blades progressed to the quarter-finals of the Capital One Cup on Tuesday night.
The striker, on as second half substitute netted after 86 minutes and in injury-time as the Blades hit back from Benik Afobe's penalty.
Boss Clough shuffled his pack again to counter losing Basham (suspended) and McCarthy (cup-tied). In total, United made five changes with McNulty, Davies, McGahey, McEveley and Reed all included from the start. Young midfielder Dimaio was amongst the Blades bench, whilst another Academy graduate, Kyle McFadzean, brother of Callum, started for the Dons.
On a big pitch, United, wearing the yellow change strip, began the brighter with Davies and Murphy noticeably sticking to particularly wide roles. It was from a Davies cross that United went close first but McNulty challenged with McFadzean and the ball squirted just past Martin's left post.
The home side had to wait until the 25th minute before registering their first chance but Bowditch's header from a Carruthers cross was weak. Howard also saved comfortable from Flanagan but despite a dearth of chances, the Blades shaded the attacking intent in the first half.
After a tepid first half, the start of the second half was more encouraging, particularly for Unitedites. On 47 minutes, after the home side failed to clear a corner, McNulty looked favourite to turn in a Murphy cross but was crowded out by two defenders - Alcock then almost connected with a Davies corner and Scougall had a shot blocked.
Murphy sliced wide from the edge of the box and then, on 53 minutes, just before being replaced, McNulty provided a cross which beat goalkeeper Martin but Scougall was surprised to see the ball reach him and headed over.
The home side's first chance of the second half arrived on the hour, Bowditch fired at Howard, as did Afobe soon afterwards, whilst the Dons also made a double change.
United undoubtedly had made the better start to the second period but it was the home side who opened the scoring at the midway point of the half. From a Carruthers pass, Alli nicked the ball ahead of Alcock and fell under the defender's challenge. Referee East immediately pointed to the spot on AFOBE converted the penalty.
Clough's response was to replace Scougall with Baxter, whilst soon after Campbell-Ryce replaced Davies as United began to force the Dons back. However, chances were again hard to come by although Higdon, Campbell-Ryce and Harris linked up well before McFadzean cleared.
Flanagan took Reed's cross of Higdon's head but from the resulting corner, the Blades levelled. With 86 minutes gone, a short set-piece routine saw Harris cross and HIGDON held off his marker whilst directing the ball home at the back post.
As extra-time approached, the final chances of normal time fell to the home side. Alli's shot from an acute angle struck the outside of a post and Afobe's mazy run ended with a weak shot which Howard claimed.
In the five minutes of added time Higdon almost connected with a Baxter free-kick but the big striker was to have a massive say in the outcome. Again from the resulting corner, delivered by Murphy, Martin made a huge mistake and HIGDON kept his composure at the back post to fire home, via a post.
For the remaining moments the Blades fans - all 1,428 of them - sung before referee East's final whistle confirmed a last eight berth.
MK Dons: Martin, Lewington, Flanagan, McFadzean, Potter, Bowditch (Powell 61), Reeves (Grigg 61), Spence, Alli, Carruthers, Afobe.
Unused: McLoughlin, Kay, Baker, Randall, Hitchcock.
Blades: Howard, Alcock, Harris, Doyle, Murphy, Scougall (Baxter 70), McNulty (Higdon 55), Davies (Campbell-Ryce 76), McGahey, McEveley, Reed.
Unused: McGinn, Turner, Kennedy, Dimaio.