Despite the Inverness side having a hatful of chances, the visitors' cutting edge counted in the end, leaving Craig Brewster's team without a home league success since April.
Bairns boss John Hughes had already stated that he'd love to follow the lead of Caley Thistle, whose attitude, hard graft and ability saw them secure eighth place in their debut SPL term last season.
They had certainly been going well until the weekend when a revitalised Dundee United beat them 3-1 at home.
The Highlanders had taken a point in the weekend's clash with Livingston, although felt they should have had more after an impressive second-half display.
This was the second meeting between the teams this season. The first on day one of the new season saw two Craig Brewster goals make all the difference.
The downpours eased in the lead-up to kick-off in a match played under Caley Thistle's shiny and ultra-powerful new floodlights.
The adverse conditions certainly seemed to affect the attendance with only 3,660 inside the Caledonian Stadium.
Falkirk's Russell Latapy went close as early as the sixth minute when he flashed a long-range free-kick just past the left post.
In response, Barry Wilson tested Matt Glennon with a 25-yarder after fine work from Dennis Wyness and Liam Fox set him up for it.
Then a great darting run from Wyness ended when his low drive swerved just beyond the far post from 20 yards.
Brewster could have fired Inverness in front soon after but he failed to control an excellent pass from Wyness.
Steven Thomson shot Bairns into a lead in controversial circumstances on 22 minutes when the forward appeared to be in an offside position when he accepted a through ball from Latapy before drilling the ball beyond Mark Brown into the goal.
Most players expected the flag to be raised but it wasn't and Falkirk accepted the good fortune much to the fury of the home supporters.
Richie Hart tested Glennon with a stooping header from a Ross Tokely cross as the hosts tried to find a way back into things before the break but the keeper got down well to hold it.
Ten minutes after the interval some superb vision from Grant Munro saw him send Wilson clear on goal but the winger sent his effort well wide of goal.
However, the Falkirk points were secured for the journey home when Duffy played an intelligent one-two with Latapy before steering the ball past Brown.
The third arrived in stoppage time when substitute Pedro Moutinho slammed an effort past Brown when he got on to John O'Neil's defence splitting pass.