The result sees Alan Maybury's men finish fourth in Group E with five points to their name. Championship outfit Arbroath go through as group winners with an unblemished record of four straight wins.
The hosts took an early lead at the SMiSA Stadium after Robbie McIntyre was adjudged to have fouled Jonah Ayunga in the box and Mark O'Hara duly converted the resulting spot-kick in the eighth minute.
Ayunga then got his name on the scoresheet in the 25th minute as the striker slotted under goalkeeper Sam Ramsbottom.
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Ayunga's second of the match a minute after the restart ensured the points would be staying in Paisley but the Capital men did find a consolation seven minutes later through a well-placed Danny Handling shot.
Maybury's side make their League One debut at Kelty Hearts next Saturday.