The Blues fielded Southend goalkeeper Luke Chambers between the posts, while ex-Northampton Town player Claudio Diaz was on the bench.
The hosts made the early running as Adam Watkins’ shot was saved, as was Jemale McKenzie-Lowe’s attempt.
Charlie Henry then had the ball in the net, but it was ruled out for offside, before Dunstable took the lead on 18 minutes.
Quick passing from Henry, Watkins and McKenzie-Lowe saw Chris Marsh receive possession and his sumptuous cross was fired home by Eliot Sandy.
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Blues then won a penalty after Watkins was brought down, but Marsh’s spot kick was saved.
In the second period, Barton drew level in the opening exchanges as Keshi Anderson finished off a move from close range.
Back came Dunstable though as they retook the lead almost immediately with Sandy on target for his second.
Marsh made way for Diaz and Terry Dixon came on for Scott Davies, the former soon involved with a typical headed opportunity, following good work from Herd and Henry.
The third arrived after 68 minutes when Dixon fired a cracking set-piece into the net from just outside the box.
Dunstable now start their Southern Premier Division campaign at Bideford this weekend.
Blues: Luke Chambers, Ben Herd, Leon Cashman, Nick Beasant, Shane Blackett, Scott Davies, Adam Watkins, Charlie Henry, Jamale McKenzie-Lowe, Eliot Sandy, Christopher Marsh.
Subs used: Terry Dixon, Ryan Plowright, Claudio Diaz.