The Blades lost ground on the play-off contenders with Wednesday night's defeat in front of the Sky Sports camera.
A first visit to Roots Hall in almost 20 years saw two second half goals condemn the Blades to defeat.
Dean Hammond cancelled out Tyrone Barnett's goal but second half efforts from David Worrall and Jack Payne secured the points for the home side.
Whiteman started, in for the injured Brayford, who picked up a calf problem in training earlier in the week. The teenager slotted into the right-wing back role. Woolford returned from injury to take a place on the bench.
The opening 15 minutes were very even with both sides recording two chances each. Coker curled a free-kick into the arms of Long and Deegan side-footed a corner routine over. For the Blades, from Done's quick throw, Sharp's half volley was pushed around a post by goalkeeper Bentley, who then kept out a Done cross and the rebound from Flynn.
On 27 minutes United came close to opening the scoring, Bentley fumbled Sharp's left-foot shot but recovered as the ball rolled towards the goal-line and within a minute Southend had grabbed the advantage. Worrall's free-kick saw Thompson's header stopped by Long but he was unable to hold and BARNETT poked from close range.
The Blades did not deserve to be behind and levelled with the next chance, with 34 minutes gone. Thompson fouled Adams on the edge of the box and with the home side expecting a shot, Flynn clipped to the back post where an unmarked HAMMOND headed home.
Late in the half the better chances dropped to the home side. McLaughlin cut inside Done but the subsequent shot was pushed away by Done and then Barnett headed wide a cross from Worrall.
The better opportunities in the early minutes of the second period were United's although the home side remained a threat and Long was forced to parry away a long-range Atkinson effort.
On 53 minutes, a mazy Adams run ended with him clipping over after Hammond recycled possession and soon after Sharp should have given the Blades the lead. From Long's early delivery, Coker fell on his backside but the leading Blades scorer could only lob onto the roof of the net with Bentley out of position.
The miss was to prove costly as Southend regained the advantage on the hour. From Deegan's pass, WORRALL cut inside Done and fired a powerful shot across Long and into the corner of the net. Just five minutes later, Deegan almost added his name to the scoresheet after United failed to clear a corner and Long also saved from Barnett's volley.
United attempted to regain momentum with shots from Whiteman and Adams, whilst Adkins threw on Calvert-Lewin and Sammon and went with a three-man forward line.
Adams curled a free-kick into the arms of Bentley in the final ten minutes and Calvert-Lewin cut in from the right and shot just over the crossbar.
A frantic last few minutes saw Barnett beat the offside trap but Long blocked with his body and then, following an Adams run, Calvert-Lewin's shot was deflected wide. From the resulting corner, with the Blades committed, a Southend break saw PAYNE get the better of Done and clip over Long and into the corner of the net with Flynn sprawling to try and clear.
Added time saw Sharp fire wide before the long-trip to Sheffield begin.
Southend: Bentley, Coker, Thompson, Worrall (Leonard 84), Payne, Weston (McQueen 67), Atkinson, McLaughlin (White 77), Barnett, Deegan, Barrett.
Unused: Smith, Hurst, Loza, Malarczyk.
Blades: Long, Basham, Flynn, Coutts (Woolford 88), Sharp, Done, McEveley, Adams, McGahey, Hammond (Calvert-Lewin 73), Whiteman (Sammon 84).
Unused: Howard, Reed, Kelly, Brooks.