Ward's 48th minute left-footer was enough to seal victory for Ian Culverhouse's side, who created a handful of decent chances to add to their lead.
Cameron Gregory made an excellent save to deny Joe Hanks - but City, who had Danny Wright sent off late on, rarely threatened against a well-drilled United side.
Ward, along with Brad Nicholson, had been recalled to the United side ahead of kick-off. Jai Rowe and Finley Thorndike were the two players to make way.
Zak Mills, back at right-back, delivered a sixth minute cross which was headed over the crossbar by Kelsey Mooney. Mills later had a drive kicked off the line by Ben Richards-Everton.
Keziah Martin was denied by a brave Louis McGrory block, who was forced off on a stretcher shortly afterwards following an accidental collision with team-mate Tyrone Duffus.
United edged ahead three minutes after the break, with WARD beating Birmingham City loanee Zach Jeacock with a powerful drive from the edge of the penalty area.
Jeacock subsequently saved well from Mooney, while Gregory excelled on the hour mark to deny Hanks.
United held on without too many scares - and City's afternoon was compounded in the final minute when Wright was handed his marching orders for throwing an arm.
Boston (4-4-2): Cameron Gregory; Zak Mills (Jai Rowe 88), Michael Bostwick, Brad Nicholson, Ethan Sephton (Dylan Hill 55); Keaton Ward, Jordan Richards, Martin Woods, Keziah Martin; Kelsey Mooney, Jimmy Knowles. Subs (not used): Tom Leak, Tom Edge, Tyler Knowles.
Gloucester (4-3-3): Zach Jeacock; Harry Leeson, Tyrone Duffus, Ben Richards-Everton, Harry Emmett; Joe Hanks, Louis McGrory (Max Ram 32), Alefe Santos; Elliott Durrell (Kai Churchley 73), Danny Wright, Harry Pinchard (Joe Parker 46). Subs (not used): Enoch Ebo Andoh, Kornell McDonald.
Referee: David Jones.
Attendance: 1,331 (25 visitors).
PIC: Tim Hoff.