Steve Lovell deservedly scored the goal the Bairns' first-half possession deserved when he flicked home in the 41st minute for his eighth of the season.
But Killie, who had passed up excellent chances through Willie Gibson and Allan Russell in the opening period, improved further after the interval and Fernandez's header after 68 minutes earned a point to leave Falkirk with just one victory from their last 11 games.
Indeed, it could have been worse for the hosts - without a home win over Killie since February 1996 - as substitute Donovan Simmonds struck the crossbar late on.
Referee Iain Brines upset both sets of players and supporters by booking eight men on an often-fiery afternoon.
Falkirk left-back Tam Scobbie was drafted into a makeshift central defensive role alongside Lee Bullen - the youngster's first start in three months - due to captain Darren Barr's suspension.
Midfielder Burton O'Brien was also ruled out, with Kevin McBride coming in.
Kilmarnock boss Jim Jefferies brought in French keeper Damien Rascle - just his fourth appearance of the season - in place of the banned Alan Combe.
Danny Invincibile and Mehdi Taouil were also absent, with Frazer Wright and Gibson restored.
After an impeccably-observed minute's silence for former Falkirk player and manager George Miller, it was the Bairns who threatened inside the first minute.
Wright failed to deal with a high ball, surrendering play on the edge of the penalty area to Michael Higdon, who fed Scott Arfield but the youngster dragged weakly past.
Scobbie had to be on his toes after 12 minutes, blocking Russell's hooked effort on the 18-yard line.
Falkirk began to press and carved out their best opening in the 26th minute.
Jackie McNamara's cross from the right was flicked on by Lovell but Higdon could only steer his 12-yard shot straight at Rascle.
Three minutes later, Kilmarnock probably should have been ahead. Fernandez robbed Arnau Riera of possession and the Spaniard played in Gibson in the inside left channel.
The winger cut inside, bore down on Robert Olejnik but dragged his effort across goal and past the far post. Russell soon headed into Olejnik's arms as Killie came more into proceedings.
Yet, an even better chance came Russell's way after 33 minutes.
Falkirk were caught on the break and Fernandez raced clear, squaring for the unmarked Russell.
But the ex-Airdrie marksman took a terrible first touch, allowing Olejnik the time to rush from his goal and block at this feet.
However, just as Jefferies' men looked to have fought back into the match, Falkirk's dominance yielded a goal four minutes from the break.
McBride's weak drive was fortuitously deflected by Grant Murray into the path of Lovell, who cleverly flicked the ball past Rascle and saw it trickle into the bottom left-hand corner.
Lovell's looping effort past the far post saw Falkirk on the front foot after the interval.
Murray came to Killie's rescue in the 52nd minute, brilliantly hooking clear from his six-yard box when Higdon looked set to net.
A scrappy match began to unfold, not helped by a spate of bookings that interrupted play as tensions grew, Lovell the seventh player to be cautioned with just 63 minutes on the clock.
Brines had been especially infuriating the away support with his decisions, but they were left celebrating after 68 minutes when Fernandez levelled.
Gibson's trickery on the right provided room for an inswinging cross Fernandez helped into the net with a neat back-header.
Strikers Simmonds and Graham Barrett came off the bench for both sides respectively late on, with the visitors looking the more likely to claim the points.
Indeed, in a frenetic closing spell, on-loan Coventry forward Simmonds was unlucky to see his powerful 80th-minute header hit the bar from Murray's cross.
Higdon headed just past at the other end, before the striker superbly nodded off his own line in injury-time to preserve a point.