Portuguese forward Pedro Moutinho curled home a sublime free-kick two minutes into first-half stoppage time, his sixth of the season, before turning provider for a scrappy second goal in the 67th minute.
St Mirren substitute Andy Dorman pulled one back in injury time but it was too little too late.
Steven Pressley's side remain bottom on goal difference, but their first back-to-back wins of the campaign have given their survival chances a massive lift and brought others into the relegation mix.
St Mirren were seeking a fourth straight success at the Falkirk Stadium, but they remain winless in the league for almost six months after a deserved triumph from the resurgent hosts.
Pressley recalled Brian McLean after suspension in place of Tam Scobbie. Kieran Duffie, the 18-year-old defender, retained his place for just a third start.
Gus MacPherson suffered a pre-match blow as ex-Bairn Jack Ross missed out with an ankle injury. Dorman dropped to the bench with Garry Brady and David Barron coming in.
A healthy crowd filtered in for a key fixture, with the Paisley support almost filling the North Stand.
The Bairns, after just two previous wins at home all season in the Clydesdale Bank Premier League, looked determined for success in the April sunshine.
They made a lively start and Scott Arfield's six-minute free-kick, which flashed two yards wide of the right post, saw them go close first.
Barron replied with a drive into a ruck of bodies, later pleading to referee Dougie McDonald for a penalty for handball, before firing the rebound high over Robert Olejnik's bar.
As the play initially excited, Duffie picked out Mark Stewart with a superb cross from the right but the striker shot just over on the volley.
The Buddies began to look more of a threat on the break with Michael Higdon, whose goal kept Falkirk up last season under John Hughes, the focal point of their attack.
It had become the scrappy, tense affair many expected, yet chances still came.
Colin Healy fed Moutinho on the edge of the penalty area but he pulled wide of the left upright.
St Mirren almost struck in the 33rd minute when Olejnik was forced to make his first save, denying Steven Thomson, another former Falkirk player, at his near post.
On the stroke of half-time, Duffie played in Arfield, whose drive was pushed clear by Paul Gallacher before Healy blazed the rebound over.
The sides looked set to go in goalless at the break but in the second minute of stoppage time Falkirk's persistence paid off.
Moutinho appeared to go to ground too easily under a challenge from St Mirren skipper John Potter some 20 yards from goal.
The pair exchanged some harsh words before the attacker dusted himself down and curled in a sweet right-footed free-kick over the wall and beyond Gallacher. As the interval whistle sounded, Potter angrily continued his protests with McDonald.
MacPherson made his first change after just 50 minutes, Dorman replacing Hugh Murray.
St Mirren were enjoying more of the ball but Falkirk were restricting them to long-range opportunities.
In fact, chances at both ends were proving elusive as a midfield battle ensued.
Then, out of nothing on 65 minutes, Falkirk struck a crucial second goal.
Moutinho's free-kick looked tame, but Darren Barr got a slight flick on the ball for it to hit Higdon and wrong-foot Gallacher.
Stewart then fired just wide from a tight angle as the home side's confidence grew.
MacPherson had seen enough and withdrew Lee Mair and Higdon on 69 minutes, as Steven Robb and Rory Loy came on.
Tensions then looked set to boil over as Barr and Billy Mehmet argued in the far corner, with Moutinho rushing over to shove the Buddies striker. Both Mehmet and Moutinho were yellow-carded.
Arfield could have added gloss to the outcome eight minutes from the end but he skewed badly wide after being set up by the impressive Ryan Flynn.
From a Chris Innes centre, Dorman headed home from point-blank range two minutes into stoppage time but Falkirk held on.
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