The atmosphere at East End Park was subdued, despite the visit of the 'Auld Enemy', in the wake of the First Division club going into interim administration earlier on Wednesday.
Players with uncertain futures still put in a determined display but they were up against it for most of the match after Lyle Taylor gave Falkirk the lead with a 10th minute header.
Ryan Wallace passed up a golden chance to level the scores midway through the first-half, but blasted his shot over the bar when it seemed easier to score.
Blair Alston fired over for the Bairns and Taylor was denied his second goal of the night just before the break when Paul Gallacher came up with a superb save down to his right.
Michael McGovern's first real save of the night denied Josh Falkingham an equaliser early in the second period and Dunfermline thought they had earned a penalty going into the final 20 minutes when Andy Barrowman went down in the box - nothing was given.
But their hopes of a point to end a trying day were dashed two minutes from time when Alston beat Gallacher to seal the points and move Falkirk within a point of Dunfermline in fourth and fifth spots.