Hibs were ahead at the interval thanks to Steven Fletcher's well-taken goal as early as the fifth minute.
But it all started to go wrong for Tony Mowbray's side when Kilmarnock were awarded a corner just after the break. Peter Leven swung the ball over and it eventually flew towards Colin Nish who leapt superbly to power in an acrobatic overhead kick which was destined for the bottom corner of the net until David Murphy stuck out his hand to block on the line.
Referee Alan Freeland had no option but to award the penalty and show Murphy the red card. Steven Naismith remained calm and sent the keeper the wrong way from the spot to equalise.
Hibs responded well to being a man down and Killie keeper Alan Combe had to produce smart saves to deny Fletcher, Gary Caldwell and Steven Whittaker.
Kilmarnock gradually took control and it was no surprise when they went ahead in the 71st minute. Leven's free-kick from the right dropped to Gordon Greer who gleefully drove the ball high into the net on the half-volley.
Hibs' young team began to lose their discipline and were made to pay in the 75th minute. Just as Hibs were about to spring a counter-attack, Caldwell cynically hauled down Fraser Wright in midfield and, instead of chasing the equaliser, they were defending deep in their box, and Nish capitlased further when he spun and shot into the roof of the net.
The referee brandished yellow card after yellow card to Hibees for dissent, before Zbigniew Malkowski gestured towards him for a second time and followed Murphy to the early bath leaving Hibs to finish with only nine men.
Naismith almost added a fourth, but saw his shot rebound off the post.