Paul Clayton was in the right place at the right time to score the last-gasp winner which moved the Lions up to 10th place and just two points off the play-off zone.
Both sides attacked from the first whistle, the hosts taking the lead thanks to a well-worked team goal. Kayode Odejayi found room and passed to Kingsley James and he fired a shot from the edge of the area into the bottom right-hand corner of the net.
Brackley equalised minutes later with a freak goal as Luke Fairlamb swung a corner in – it was picked up by the wind and flew into the top corner.
Kevin Wilkin’s side were clearly buoyed by drawing level as they nearly took the lead. Shaun Jeffers worked some room for himself and hit the post on the angle.
The conditions didn’t improve during the game with the wind playing a big part in the pace of the match, as it slowed down and chances were then at a premium. Brackley came close to taking the lead, when Fairlamb collected a pass and after a strong run into the area, forced Guiseley keeper Joe Green into a smart save.
The Lions began to press with time running out but the bounce of the ball wasn’t going their way though.
It looked like the game would end a draw, until a late Alex Purver cross wasn’t held and the ball fell to Clayton who had a tap-in from two yards out.
Guiseley joint manager Marcus Bignot was delighted with the three points. He said: “It is a really good feeling to win so late.
“We’ve played a good side who have plenty of experience and that is an important three points for us.
“We got a lot of the basics right and it’s another performance where we can be pleased with what we have done.”
Bradford Park Avenue went down at home to title hopefuls Kidderminster following two late Ed Williams goals.
After Luca Havern cleared James O’Connor’s header off the line, Avenue took a second-half lead when Conor Branson rifled in.
Oli Johnson then hit a post for the home team, but England C international Williams levelled with nine minutes left when he cut in from the right and curled into the bottom corner.
On 89 minutes, Williams settled matters with his tenth goal of the season, gliding past three players before finding the bottom corner again.
Elsewhere, Sam Collins won his first game in permanent charge of York City as the Minstermen won 2-1 at second-bottom Southport.