Substitute Michael Higdon equalised for the Bairns early in the second half when he headed past Tomas Cerny.
The Bairns were also failing to cope with McCarthy's free role behind lone striker Joel Thomas.
But it was the Bairns who went ahead against the run of play after 16 minutes.
But, soon after, the Bairns were back on level terms thanks to a wonderful volley from Holden.
Killie need to avoid defeat against Falkirk on Saturday to secure SPL status and send the Bairns down.
Andrius Velicka's solitary goal sealed the win over the Bairns, days after Kanuas knocked Rangers out of Europe.
But at half-time, with the Bairns goalless against St Johnstone, Killie had moved to the bottom of the table.
The 22-year-old, who began his career at Rangers, left the Bairns two years ago in search of first team football.
Hughes is on the lookout for a challenge to Yves Ma-Kalamby and Mallo is out of contract with the Bairns.
But it was the visitors who threatened early on with Lafferty causing the Bairns defence problems on the left wing.
Sadly for the Bairns, that particular foray ended in ignominy at the first hurdle with that defeat by Vaduz of Liechtenstein.
But the Bairns were playing with a swagger and ended any lingering hopes of an Aberdeen comeback with 20 minutes remaining.
Kieran Duffy was preferred to former Don Jackie McNamara in the Bairns defence and Carl Finnigan starting ahead of Jack Compton.
The Bairns had the ball in the net after 77 minutes, but Finnigan had clearly barged goalkeeper Combe over the line.
Pressley took over from Eddie May in February and took the Bairns' fight against relegation until the last day of the season.
And Driver weaved through the Bairns defence to score after the break.
The Bairns enjoyed the lion's share of possession from defence through midfield but could not create the clear-cut chances their build-up play merited.
Kilmarnock escaped relegation on the final day of the season, a 0-0 draw away to Falkirk sending the Bairns down to Division One.
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Two minutes later, the Bairns sealed all three points with a third when Cerny was culpable with a poor clearance straight to O'Brien.
Hughes, who has a year of his Falkirk contract to run, came in for flak from fans this season as the Bairns battled against relegation.
Falkirk boss John Hughes did state his interest in taking charge at the Liberty Stadium, but has since left the Bairns to take over at Hibernian.
But the Bairns came roaring back before the break with a cool finish from Pedro Moutinho levelling matters and Darren Barr's header putting them in front.
Ryan Flynn missed a great late chance for the Bairns and the draw was enough for Kilmarnock to extend their 17-year run in Scotland's top flight.
Against the run of play however, Finnigan grabbed an equaliser from Dean Holden's knock-down with a fine turn and shot which brought the Bairns back into the game.
Finally, Motherwell host Falkirk, with Mark McGhee's team enjoying a fine run of form, while the Bairns haven't won a league game since 15 November - against today's opponents.
The Bairns were the brighter team in the opening 45 minutes, with Neil McCann twice going close, while Steve Lovell hit the post during Falkirk's late bid to salvage the tie.
Mallo was signed by Hughes for the Bairns midway through last season and the new Hibs boss has already been reunited with two former Falkirk players in midfielders Patrick Cregg and Kevin McBride.
The Frenchman headed David Graham's cross against Olejnik's right-hand post with what looked like the aid of a touch from the Falkirk keeper and the Bairns won the ensuing scramble for the loose ball.
It was his successful loan spell as a teenager under Hughes when the Hibs boss was in charge of the Bairns that led then Sunderland manager Roy Keane to move for the young prospect.
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