Both sides struggled to create good openings at Rugby Park
Jamie Hamill scored a late winning goal for Kilmarnock five minutes after coming on as a substitute.
The midfielder drilled in a sweet strike from 20 yards to settle a low quality game packed full of endeavour.
Colin Nish wasted a great early chance for Hibs, shooting tamely at Killie goalkeeper Alan Combe.
The home custodian also made good stops to deny Steven Fletcher and Filipe Morais, while Mehdi Taouil and Danny Invincibile went close for Killie.
Carrying on their form from last season, Kilmarnock have now gone seven games unbeaten at Rugby Park but there was little between the sides.
The visitors started brightly and Nish was guilty of missing a glaring chance against his former club.
Fletcher robbed the dithering Gary Hay to set up his strike partner but the gangly forward trundled his shot from 10 yards straight at Combe.
Moments later, Combe made a fine diving save from Fletcher after the Scotland international turned defender Simon Ford with a clever flick.
There were a lot of full-blooded challenges to keep the fans entertained but Killie lost Ryan O'Leary to injury, while Hibs' summer recruit Steven Thicot also had to be replaced before the interval.
In the 31st minute Killie's talented playmaker Taouil picked up a Jamie Fowler pass, skipped past defender Chris Hogg and fired in a tremendous right-footed drive from 30 yards, which Hibs keeper Andy McNeil did well to tip over the bar.
Substitute Frazer Wright then saw his shot deflected wide after McNeil flapped unconvincingly at a corner.
Kilmarnock finished the half strongly but just before the break Combe was in good position to deal with a strike from Hibs substitute Ross Chisholm.
Both sides continued to expend a lot of energy as the second half opened at a whirlwind pace but there was a lack of composure in the final third.
Hibernian's teenage full-back Paul Hanlon saw his long-range shot whistle over the crossbar, while Nish inadvertently helped out his old team by getting in the way of a goal-bound nod from Hogg.
Hamill celebrates his winning strike on 80 minutes
Rob Jones had flicked on for his defensive colleague and when the ball struck Nish, the Hibs skipper could only fire the loose ball into the side-netting.
Kilmarnock midfielder Craig Bryson was given a round of applause for a powerful shot that went too high but his well placed team-mates on the edge of the penalty area didn't look too happy.
Combe made a fine save to keep out shot from Filipe Morais and Hay was on hand to make a smart clearance before Fabian Yantorno could pounce.
Having used all their substitutes, Hibs were down to 10 men when David van Zanten left the field with blood flooding from a facial injury.
Killie immediately sensed an advantage and visiting keeper McNeil didn't know too much about Invicibile's shot, which struck him on the hip and bounced away to safety.
Chisholm moved from his central midfield role to cover for right-back van Zanten and the gap was exploited when Hamill struck soon after coming off the bench.
With ten minutes remaining, Hamill picked up a pass from David Fernandez and steered an excellent low shot into the corner of the net from 20 yards.
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