Manager Gary Johnson made four changes with Chris Weale, Kevin Dawson, Nathan Ralph, Ajay Leitch-Smith all started in the place of Artur Krysiak, Nana Twumasi, James Berrett and James Hayter.
In a quiet start the home side was forced to make an early change after defender Hare was forced off on a stretcher to be replaced by Fish.
In the twelfth minute Leitch-Smith picked up the ball on the wing and cut in on his right foot, the former Crewe man shot from the edge of the area but Bywater saved well after the initial shot was deflected.
Five minutes later Town had the ideal opportunity to take the lead. Nugent went forward for an attacking throw in and was upended in the box by Legge. After a short conversation between Moore and Simon Gillett the penalty duty was left to Moore.
The former Dorchester man stepped up but saw his penalty saved by debutant Stephen Bywater in the Gillingham goal.
Town fell behind with ten minutes of the first half remaining. A harsh free kick was awarded by referee Lee Collins after he adjusted Nathan Smith had fouled Kedwell.
At half time Town made one change with Moore being replaced by James Hayter.
Ten minutes into the second half the home side doubled their advantage after Nathan Smith fouled Aaron Morris inside the area resulting in a penalty. Kedwell’s penalty was well saved by Weale, but the ball fell to Kedwell who had the easy task of slotting home to make it 2-0 to send Town back to Somerset empty handed.