Barnsley 1 (Waring 56)
Barnsley made it three wins on the bounce as well as three clean sheets in a row to finish the afternoon in the top half of the League One table.
Lee Johnson made two changes for his first match in charge with Milan Lalkovic replacing James Bailey and Mason Holgate coming in for the suspended Jean-Yves M'voto.
The weather conditions didn't help this encounter in the first half with clear cut chances at a premium.
It took five minutes for some real action when Jermaine McGlashan stole a yard on George Smith and he eventually put in a cross but Barnsley were able to clear any potential danger.
The blustery conditions were making it difficult for both sides.
Gillingham were trying to use McGlashan as their main outlet for attacking in the early exchanges but there were few chance for either side.
The Reds were patiently trying to find a way around the Gillingham defence and enjoyed a large amount of possession, but found it hard to find the key to unlock their defence.
Barnsley's first corner came on 20 minutes for Scowen to loft the ball into the box but despite Waring's climbing leap, Gillingham were able to clear.
Waring got a good header in to let Lalkovic get into the Gills box but Egan got a foot on the ball to deny Milan from getting an opportunity.
A well timed tackle by Nyatanga on 22 minutes in the box prevented Cody McDonald from getting a shot in the Barnsley box.
On 25 minutes O'Sullivan's attacking run into the box came out nicely for Scowen to shot but his attempt was off target.
Barnsley lost possession in attack when Mason Holgate's pass was intercepted and McGlashan tried to trick his way around George Smith who was able to deflect his cross out for a corner. The Gills could not make anything from it as again the conditions didn't help.
A Pearson foul on 31 minutes gave Gillingham a free kick just 24 yards out. It was Bradley Dack who took it but his strike was well wide.
On 36 minutes McGlashan got away from Smith to run at the Barnsley goal but his cross went across the face of goal with no Gillingham player to get onto it and it ended up a Barnsley goal kick.
A couple of minutes later McGlashan again put a ball in for Marquis to head at goal which rebounded off Nyatanga and into the arms of Davies.
Persistence from Lalkovic at the byline earned the Reds a corner despite Egan's protests. Scone put the ball in which was claimed by Nelson in goal.
A good Barnsley move on 45 minutes ended with a ball high over. Hourihane had put in a great ball for O'Sullivan who placed his pass to Scowen but his shot was well over.
With just one added minute at the end of the first half Gillingham had a free kick, after a Pearson foul who received a yellow card for his troubles, but the ball found its way to Davies.
In the opening minute of the second half Adam Davies had to rush out of the box to clear the ball but got caught by McDonald for a Barnsley free kick.
Milan Lalkovic looked to have put George Waring through on goal but the ball was intercepted, although looked like a hand ball as the Barnsley pair protested.
It was a bright start for the Reds and Waring played Scowen in toward the corner who fed Lalkovic who ran into the box with a step over but lost his footing and stumbled over.
On 55 Barnsley looked to have carved out a decent chance when Waring, in the box, passed to Hourihane put his shot was blocked, but 30 seconds later Waring was in the right place at the right time to blast the ball into the Gillingham net from point blank range. Pearson's shot was parried by Nelson to fall nice for the Stoke City loanee to get his second Barnsley goal.
Within two minutes Gillingham were nearly level after Hoyte's shot was parried by Davies and McDonald hooked the ball over the goal from a few feet out, but fortunately for him the linesman flagged for offside.
On 64 Marquis was adjudged to have been fouled by Scowen 35 yards out but when the set piece was floated in Gillingham had strayed offside.
Gillingham stepped up the pressure in search of an equaliser whilst Barnsley were trying to find a second goal to give them some security in the game. With both sides looking to attack in the final 20 minutes the play was opening up.
With just 13 minutes remaining Gillingham got two quick corners, but Gillingham could not make the set piece count.
On 87 John O'Sullivan struck a great shot which Nelson managed to get his fingertips to save.
In injury time Bradley Dack put McGlashan through on goal with just Davies to beat but the Barnsley keeper made a superb save. Dack was nearly in a minute later but Nyatanga's challenge was timely.
With space opening up Hourihane had a shot on target but he hit it straight at the keeper.
A final minute corner for Gillingham was not enough and Barnsley held out for the win.
Gillingham: Nelson, Garmston (Martin 57), Egan, Ehmer, Loft (C), Hessenthaler (Norris 66), Marquis, McDonald, McGlashan, Dack, Hoyte (Galbraith 81).
Subs: Legge, G Morris, A Morris, Romeo.
Barnsley: Davies, Holgate, Cranie (C), Nyatanga, Smith, Lalkovic, Scowen, Pearson, Hourihane, O'Sullivan (Bailey 88), Waring (Oates 90).
Subs: Dibble, Williams, Lita, Hemmings, Berry
Attendance: 5,905 (377 Reds)