United's total dominance of this game was finally rewarded in the seventh of six minutes of added time.
Jamie Murphy's mazy run ended with him slotting through the legs of Gillingham goalkeeper, Stephen Bywater.
In a game that saw United have 27 shots and 16 corners, Gillingham thought they had smashed and grabbed with Luke Norris scoring but Michael Higdon levelled and then laid on the winner for Murphy.
Boss Clough made a total of five changes. Doyle returned to captain the side, there were also recalls for Davies, Scougall, McNulty and McEveley. The early indications were that McNulty was the most advanced, supported by Murphy and Davies from the flanks.
On the left, Murphy saw a lot of early ball and forced the first corner, from which McEveley's flicked header from a Davies delivery was wide. Davies then robbed former Blades loanee Egan but the subsequent shot from a narrow angle was saved.
Gillingham survived United's initial burst and then put the Blades defence under pressure. Howard was unduly worried and the home side were quickly back on the attack. Murphy delivered a couple more tempting crosses and on 20 minutes Wallace's half volley from the edge of the box was just wide. A succession of Davies corners failed to break the deadlock and a 25-yard shot from Doyle stung the palms of Bywater.
The visiting side's disciplined defensive unit were making it difficult for the Blades, despite Murphy and Davies looking threatening and McNulty linking up play well. Another Davies corner, on 34 minutes, saw Wallace connect but Hoyte headed clear from in front of his goalkeeper.
As half-time approached, McNulty's run across the edge of the box saw him win a corner and leave two Gillingham players on the floor, whilst the visitors created two late half-chances but Dickenson and McDonald were off target.
In injury-time United's best chance of the period also failed to open the scoring. From yet another Davies corner, McEveley won the initial header but McNulty's pounce was pushed out by Bywater and McGahey's rebound was cleared off the line by Linganzi.
The Blades also started the second half well with Wallace at the heart of a couple of moves. On 51 minutes he won possession, drove at the defence and played in McNulty, who committed Bywater before Callum Davies cleared off the line.
United, kicking towards the Kop, continued to force the visitors back. Scougall scuffed a shot from a Davies corner and Wallace's header, from Alcock's cross on 61 minutes, was pushed over the top by Bywater.
Goalkeeper Bywater was United's scourge again on 65 minutes. He blocked from Scougall after the Scotsman was picked out by Wallace and McNulty was adjudged to be offside as he followed up.
After a spell of substitutions, including the introduction of Harris and Flynn, Gillingham's first chance of the second half arrived when Loft's shot was on target but comfortable for Harris. On 73 minutes, United's agony continued. Wallace was committed and won a challenge with Linganzi to set up McNulty, whose effort struck a post. It was the last contribution of the limping McNulty, who was replaced by Higdon. Martin also did well to beat Alcock to a Harris cross moments later.
Higdon struck the same post as McNulty on 78 minutes following Alcock's cross and another Scougall effort was blocked. Bywater was booked for wasting time and United's failure to score, despite totally dominating was compounded on 83 minutes. From a throw on the left, substitute NORRIS turned and half-volleyed past Howard and in, via the underside of the crossbar.
Bramall Lane was stunned and the crowd were understandably quiet...until 87 minutes when the leveller arrived. Alcock was giving the space to attack down the right and his low front post cross was turned in by HIGDON.
Six minutes of added time - mainly due to Gillingham slowing down the action at every juncture - gave the Blades fans more cause for optimism but the visiting defence were resolute and the only chance of note was a Higdon free-kick which struck the wall...until the seventh minute of six minutes of injury-time.
The Blades almost caused themselves problems at the back but as the clock ticked, on Harris launched forward, Higdon laid off and MURPHY went on a mazy run before slotting the ball through goalkeeper Bywater's legs. Wow.
Blades: Howard, Alcock, Wallace, Doyle, Murphy, Scougall, McNulty (Higdon 75), Collins, Davies (Flynn 69), McGahey, McEveley (Harris 69).
Unused: Basham, Porter, Reed, Turner.
Gillingham: Bywater, Martin, Egan, Hause, Loft, McDonald (Norris 69), Linganzi (Hessenthaler 90), Pritchard, Davies, Dickenson, Hoyte.
Unused: Fish, McGlashan, Morris, German, Dack.