George Newell's late winner was enough to secure all three points in a spirited performance by Colin Caton's men who were a man down on Friday night.
The Lakesiders rallied together after an early setback with Nathan Peate being sent off following a scuffle in the area.
Despite the disadvantage, Bala looked the better side as they pushed for an opener throughout the second half and managed to grab one via the head of Newell late on.
Peate sees red
A bright start from the Lakesiders saw them push the pace from the start with both sides having half chances to take the lead throughout the opening twenty minutes.
The first significant moment of the match came a third of the way in when a push and nothing more from Peate led to the referee curiously reaching for a straight red card.
The match comes to life
After a half of no chances to note, the match finally kicked into action shortly after the break. Flint's first clear-cut opportunity fell to a free Silkman in the area from a corner, but he was unable to direct a header on target as it crawled past the post.
A couple of moments later another chance fell their way with the ball falling kindly on the edge of the area to be struck before it was ballooned over the bar.
From here, the Lakesiders took over. Adam Roscrow had appeared to put us in front just past the hour mark with his celebrations cut short following a tidy finish as the linesman had his flag up to call for a handball.
It was then our other forward who went close as George Newell was denied from close range from a dramatic block at the back stick following a cross into the area.
Mendes and Newell round the goalkeeper, but can't finish the job!
With just over ten minutes remaining, Bala continued to push for an opener. Lassana Mendes looked certain to provide it after he latched onto a long ball and rounded the goalkeeper only to see his effort towards goal blocked by a last-ditch block.
It was déjà vu for the Lakesiders moments later as Newell also looked to have left the keeper for dead in a one-on-one situation, but the Silkmen shot-stopper was able to make up for his error and prevent our No27 from finding the back of the net.
If at first, you don't succeed, try and try again
The Lakesiders were finally rewarded for all their hard work with little time remaining when Newell popped up (quite literally) with the winner. An inch-perfect cross swept into the area by Luke Wall was met by the awaiting head of the striker who guided the ball past Allen and sent the Bala fans wild.
Edwards makes a goal-line clearance to secure the win!
To conclude the game it was Dave Edwards - who had been filling in at CB following Peate's dismissal - who made himself a hero with his goal-line clearance in the dying moments of the game to secure all three points for his side.
Up next for the Town is a trip to South Wales as we take on Pontypridd Town at the USW Sports Park next Sunday, 14:30.
Bala Town - Alex Ramsay, Naim Arsan, Nathan Peate, Ross White, Oliver Southern, Kieran Smith, Dave Edwards, George Newell, Paul Rutherford, Lassana Mendes, Adam Roscrow
Flint Town -Harry Allen, Omar Ibrahim, Anthony Stephens, Harry Owen, Daniel Harrison, Larnell Cole, James Owen, Mark Cadwallader, Omari Simmonds, Berti Diau, Jean-Louis Akpa--Akpro
Bala Town - George Newell (82)
Bala Town - James Davies > Paul Rutherford (63), Ollie Shannon > Adam Roscrow (63), Luke Wall > Oliver Southern (67), Ethan Jones > Lassana Mendes (91)
Flint Town - Jordan Carroll > James Owen (35), Ben Hughes > Okera Simmons (48)