Goals early in each half condemned the Blades to defeat at Bramall Lane on Saturday.
Co-owners Kevin McCabe and Prince Abdullah were in attendance but Chris Porter's first half header was not enough.
Danny Kedwell capitalised on a mistake to give Gillingham the lead and Cody McDonald added number two just after the break.
Boss Clough made two changes to the United line up for Sky Bet League One encounter with White and Flynn recalled, McGinn and Coady dropping to the bench. The personnel changes saw Lappin move into central midfield and White ahead of Hill on the left.
An early long throw-in from Hewitt displayed that Gillingham could be a threat but they were gifted the opening goal on seven minutes. A back-pass from Maguire was short and KEDWELL's challenge with Long resulted in the ball dribbling over the line in front of the Kop fans.
The goal served to spur the Blades and the remainder of the half was largely played heading towards the Gillingham goal. Porter beat goalkeeper Nelson to Lappin's cross but headed wide and then a shot from Lappin was deflected wide on 16 minutes.
Maguire came within inches of making amends when his header from a Lappin corner was cleared off the line by Hewitt. However, Lappin's set-piece deliveries were causing problems and United made one pay on 18 minutes when Porter rose highest to power home a corner from close range.
Before the restart Gillingham were forced to make their second substitute of the fixture through injury, the second of which was scorer Kedwell, who was struggling from the moment he collided with Long during the goal incident.
Miller twice went close to giving the Blades the lead. He curled wide after Flynn had dispossessed Hollands and then the striker was unable to get the required power to trouble Nelson after McMahon's pass.
Gillingham had the final chance of the half, though, in injury-time, when substitute McDonald looked to use his pace to get away from the Blades defence but Collins kept his eye on the ball and timed his tackle perfectly in the penalty area.
As in the first half, the visitors were quicker out of the blocks and were rewarded with a second goal just moments after the interval. Nelson's long free-kick saw Mousinho's header hit the crossbar and strike Long but McDONALD was ideally position to poke home the rebound, albeit at the second attempt.
Further Lappin corners were causing problems for the Gillingham defence before he was replaced by Baxter, who threaded a pass for McMahon, which almost brought the Blades a second leveller.
Miller fired across goal and just wide on 68 minutes, whilst Clough shuffled his players and brought on McGinn for Hill. Porter fired over from 20 yards after linking up with McGinn and then flicked a header from Doyle's cross just wide.
The final roll of the dice for the Blades management was to introduce Taylor for Flynn and revert to three at the back as the final ten minutes approached.
Expectedly, the Blades were dominating the closing stages, searching for another equaliser. A McGinn free-kick caused a melee and helped Gillingham, whilst four added minutes buoyed the home fans.
Miller was booked for an alleged foul on Nelson, who soaked up time by receiving treatment, and Baxter was also shown a yellow card for a lunge at Weston as time finally ran out
Blades: Long, White, Maguire, Hill (McGinn 72), Flynn (Taylor 79), Doyle, Porter, Miller, Collins, Lappin (Baxter 64), McMahon.
Unused: Howard, Cuvelier, Coady, King.
Gillingham: Nelson, Martin, Legge, Whelpdale, Kedwell (McDonald 18), Gregory (Dack 14), Hollands, Barrett, Fagan (Weston 79), Hewitt, Mousinho
Unused: Davies, Akinfenwa, Howard, Hessenthaler.