Southwell settled a tight affair with a 68th minute rocket which nestled into the net via a deflection off Gloucester City defender Sam Avery.
Jay Rollins also rattled the post for the Pilgrims, who were good value for their victory in the baking August sunshine.
Henrich Ravas kept United's first clean sheet of the league season after being recalled to the Boston goal with Jason Alexander suffering from a dead leg.
Zak Mills also started, with Grant Roberts making way, and aside from a couple of early long throws from Mills, noteworthy action was at a premium.
Jasbir Singh, so often United's nemesis during his Solihull Moors days, threatened to frustrate the Pilgrims once again and he produced a decent 25th minute save at the back post to deny Rollins. Southwell's first time shot then skidded wide following Kyle Dixon's low corner.
City's best first half chance fell to full-back Billy Jones, who crashed a 22-yard free-kick agonisingly wide of Ravas' right-hand upright.
United survived the loss of Mills to injury eight minutes into the half to carve out a number of chances, with Mark Jones denied by a terrific Marc Richards block, while Singh denied Rollins following Jamie McGhee's pinpoint assist.
Rollins' angled drive bounced to safety off the post with Singh beaten before the City keeper saved superbly from Mark Jones and Carl Piergianni had an effort cleared off the line by Mike Green.
United finally took the lead with 22 minutes remaining when SOUTHWELL drove goalwards from outside the box and the ball nicked off Avery and flew into the top corner beyond Singh's grasp.
The goal sprung an otherwise conservative City side into action and Avery nestled a header narrowly wide following Billy Jones' deep corner while Ravas was called upon to deny Gloucester's set-piece specialist whose inswinging free-kick had evaded everybody and appeared set for the top corner.
Mike Symons and substitute Lewis Hall glanced late headers wide for City, but United held on.
Boston (4-4-2): Henrich Ravas; Liam Marrs, Zak Mills (Jay Dowie 54), Carl Piergianni, Aziz Deen-Conteh; Jay Rollins (Jack Friend 89), Scott Garner, Kyle Dixon, Jamie McGhee (Jordan Deacey 76); Dayle Southwell, Mark Jones. Subs (not used): Grant Roberts, Jason Alexander (gk).
Gloucester (4-3-3): Jasbir Singh; Mike Green, Matt Williams, Sam Avery, Billy Jones; Mat Liddiard, Marc Richards (Adam Connolly 65), Joe Hanks; Harry White (Connor Thompson 73), Mike Symons, Joe Parker (Lewis Hall 65). Subs (not used): Sammie Hicks, Spencer Hamilton.
Referee: Neil Hair.
Attendance: 990 (16 visitors).