Goals at the start and end of the second half took Long Melford through to the first round of the Thurlow Nunn League Cup.
Matt Hayden put the Premier Division side ahead in the 50th minute and with time almost up Melford substitute Will Finch killed the preliminary round tie off with a second goal.
Melford now go on to face AFC Sudbury Reserves away in the First Round on October 13.
The defeat means Borough have now been defeated at the first stage of all three cup competitions they have played in this season; the FA Cup, FA Vase and the League Cup.
Borough’s next match is at home to March Town United in the First Division on Saturday (3pm).