Alex Lawless’s side led 2-0 thanks to goals from Will Houghton and Tyrell Giwa before the home side reduced the deficit.
However Jamie Odegah added a third goal to secure the Town youngsters their second win over their opponents having won on the opening day of the campaign.
This coming Saturday the Hatters entertain league leaders AFC Wimbledon knowing a victory will take them above the Dons to the top of the table. Kick-off at The Brache is at 11am.
Town: Hockey, Giwa, Harvey, Martins, Kayibanda, Routh, Lorentzen-Jones, Stitt, Houghton, Shephard, Odegah.
Subs: Xavier-Jones, Anderson, Benagr, Chigozie, Pipa.