A goal in each half for Nuneaton was enough to send Trinity home empty handed from Warwickshire.
Goals from Aaron Williams and Shane Byrne sent the Liberty Way faithful home happy as they made the better of the conditions on a windy afternoon.
Speaking after the game boss Steve Housham believed his side to be unfortunate.
He said: “It’s always disappointing when you lose games of football. I think in the last 20 minutes we lost that belief but we did alright barring the first goal.
“We were playing well and we gave a childish goal away, asking for offside when he’s run from his own half and that was the only chance they had first half.
“Barring the last 20 minutes, we competed. I can’t hold my hands up and say they were miles better than us.
“Yeah it could have been three or four in the second half but that was the first time that I can say that in the last 20 or 30 minutes we lost a bit of belief and looked tired and leggy.
“I felt for them because you hold your hands up and say it was a sloppy goal, come in at 0-0 it’s a totally different game. We didn’t come here for a draw, we came to win. We had three strikers on the pitch.
“We came here to be brave and we knew they would pass the ball a lot. That first goal deflated us and the second knocked the stuffing out.”
The day had began brightly for Blues fans as first choice centre half pairing Adam Quinn and Jake Picton both returned from injury to start against Boro.
Matt Wilson who had deputised at the heart of the defence, injured his back in training in the week and to compound that Stephen Brogan, who was meant to start at left back, injured a groin in the warm up.
Charlie Binns replaced Brogan in the starting lineup, leaving the Blues with only four subs on the bench.
Despite the drama, Gainsborough managed to fashion an opening in the first minute as a Simon Russell cross was glanced wide by the head of Nick Bignall.
The home side had to wait ten minutes for their first look at goal. Right back James Clifton burst into the box and hit a firm left footed strike into the side netting at the near post.
The Blues were moving the ball swiftly around the pitch, especially on the counter when they could use Bignall’s pace and it was the former Reading man who forced Jordan Smith into action with a low drive.
Marc Newsham was the next to have an attempt when he ran onto a Danny Forrest flick on. Newsham tried to clip it over Smith as the keeper closed him down and promptly denied him a goal.
In the 36th minute Nuneaton took the lead and it came from a Trinity free kick high in their half.
The delivery was headed clear and midfielder David Morgan picked up the ball, got his head up and clipped a ball over the defence for Aaron Williams to chase. Williams was in acres of space charging down on Jan Budtz with defenders in his wake and he passed the ball into the net to give Town the lead.
Boro almost increased their lead with a carbon copy of the goal with Morgan this time having a strike from the edge of the box that Budtz saved.
Nuneaton had a further chance to stretch their lead just after half time. The ball dropped to centre half Jordan Keane from a corner and he swung a left foot at it and cleared the crossbar from around the penalty spot.
The pressure continued from the home side and it was the turn of Rob Duffy to test Budtz, as his far post header was stopped by the Danish keeper.
It did not take much longer for the lead to become two as Shane Byrne drove at the Trinity defence in the 60th minute and hit a shot from the edge of the box that took a big deflection to elude Budtz.
Boro nearly added a third when Williams ran behind the defence once more. Budtz closed him down and made an excellent save before Picton managed to clear off the line as Williams looked to tap home.
Manager Steve Housham made late changes to try and swing the game in the Blues favour with Cameron Rigby making a few smart runs and Darryn Stamp coming closest with a deflected shot.
Gainsborough Trinity: Budtz, Roma, Lacey, Picton, Quinn, Binns (Stamp 58), Russell, D’Laryea, Bignall, Newsham (Yates 70), Forrest (Rigby 74). Subs (not used): Karkach.
Nuneaton Town: Smith, Clifton, Reid, J Keane, Maguire, Lane, Morgan (Dyer 70), Whitehouse (Chettle 90), Duffy (Harewood 82), Byrne, Williams. Subs (not used): C Keane, Daniels.
Goalscorers: Williams 36, Byrne 60.
Referee: Mr A Tankard. Assistants: Mr C Hunter, Mr E Cook.