An evenly contested first half saw United have the more clear cut chances. Aylesbury's best chance of the match came after just six minutes, as Martyrs keeper Ashley Morris brilliantly tipped Paul Edgeworth's header from point blank range onto the crossbar.
Towards the end of the half Aylesbury struck the woodwork again, as Danny Mead's fierce free kick from out wide struck the far post, and Leon Gutzmore was unable to react quickly enough to turn the ball into the empty net.
The second half saw Merthyr in the ascendancy, and they took the lead on 64 minutes as Chris Bale played a corner to Craig Steins on the edge of the area, and his shot took a heavy deflection before looping into the net.
Despite the Ducks putting pressure on the Martyrs with set pieces of their own - Jay Gould dropping two corner kicks right under the crossbar, and Mead forcing Morris into another brilliant save with his second dangerous freekick - it was to be Merthyr's day and they clinched the result three minutes from time.
Again Bale's set piece found Steins, and the striker nonchalantly flicked the ball into the far corner to give the scoreline a rather harsh look from a Ducks viewpoint.
Leon O'Sullivan
Merthyr Tydfil
Aylesbury United
Cirencester Town
Bedford Town
Stamford
Hemel Hempstead Town
Histon
Team Bath
Banbury United
Tiverton Town
Hitchin Town
Gloucester City
Bath City
Rugby United
Halesowen Town
Chesham United
King's Lynn
Solihull Borough
Chippenham Town
Hednesford Town
Dunstable Town
Grantham Town