The match was played in horrendous conditions as gale-force winds swept across the stadium, but it was the Bairns who mastered the conditions and played the better football.
But they almost threw the win away as Steve Lovell lost his discipline completely and saw his side reduced to 10 men for the last quarter after he assaulted Jamie Hamill after the pair tussled for the ball.
Falkirk had the ball in the net inside sixty seconds, but Neil McCann was ruled offside as he slid the ball home.
Kilmarnock's Conor Sammon threatened in the 12th minute, but Scott Flinders saved his powerful header.
The weather played a part in Falkirk's opener as Killie keeper Alan Combe fluffed an attempted clearing punch.
The ball failed to clear the area and was nodded back into the danger zone for Lovell to fire home.
The goal was no less than Falkirk deserved for their first-half pressure.
Killie almost equalised two minutes into the second half when Craig Bryson met Danny Invincibile's deep cross, but his shot rebounded off the post.
The game looked to have been settled in the 65th minute when Falkirk were awarded a penalty.
Graham Barrett was brought down by Hamill and Scott Arfield capped an excellent display as he sent Combe the wrong way from the spot.
The match then erupted in a furious flashpoint as Lovell reacted to a Hamill challenge and kneed the defender to the ground and followed up with a punch and was promptly sent off.
Killie upped the tempo and David Lilley and Sammon both shaved the woodwork as they pressed for a way back into the match.
Falkirk defended manfully and were determined to record an important win after two successive defeats.
Kilmarnock couldn't make the most of the man advantage until the match was in injury time when substitute Donovan Simmonds nodded Willie Gibson's cross home for a goal which was scant consolation.