Steve Kittrick's men showed bags of character to hang on for the success, especially as they were forced to hang on for dear life in the final moments.
Boro's preparations weren't ideal, with Tom White limping out of the pre-match warm-up to be replaced in the starting 11 by James Cadman.
Despite the late change, Boro looked to have made the ideal start when James Walshaw bundled home a Michael Coulson corner after just a matter of seconds, but referee Lewis Smith ruled out the goal citing a shove on a home defender.
A series of half-chances followed for both sides, the best seeing Max Wright drive in a cross that was glanced just wide of the far post by Boro striker Walshaw.
It seemed as though Boro had opened the scoring on the half-hour when the striker wriggled into a bit of space after a melee in the box. His shot smashed into the top of the sidenetting, with a number of travelling fans celebrating as it looked as though the finish had gone in.
Trafford created the next big opening, with Dominic McHale shaking off a couple of challenges just inside the box. Dave Merris tracked is run though and took the ball off his toe just as the striker was poised to pull the trigger.
After what was a rather large scare for the visitors, Boro finally managed to grab a cushion just before the break.
Coulson whipped a corner to the far post and Walshaw rose head and shoulders above everyone else to power the ball into the top corner.
Having finished the half with a bang, Boro started the new period in equally impressive style.
Some neat play on the left from Coulson and Walshaw saw the latter guide the ball to the far post. Trafford full-back Lee Neville had a rush of blood to the head and he volleyed the ball sweetly into his own net.
A third should have followed when Wright skipped around the keeper, but had his shot blocked. The rebound fell to Walshaw, but with Trafford bodies on the line, the effort hit a wall of white.
Trafford began to creep their way back into things as time moved on and they were unlucky not to trim the lead on the hour when Aaron Burns struck the foot of the post after a swift counter.
They did make it 2-1 minutes later, with Declan Rydings sweeping a cross from the right past a stranded Tommy Taylor.
And a levelling goal nearly followed when Jack Dorney rose unchallenged, but his header from a corner was inches wide.
Finding themselves on the back foot, Boro's hopes were stung further with 15 minutes remaining when sub Jimmy Beadle was given a straight red card for jumping into a challenge.
The ten men began to look fragile within a matter of seconds, as McHale spun in the box, but scuffed just wide.
Trafford tried to up their threat levels further by throwing on a number of subs, including towering striker Mark Derbyshire.
Battered and bruised, Boro gritted their teeth and stuck to the task, managing to hang on for the final few minutes to claim a massive three-point haul, which, at the end of the season, could prove vital.