Curtis Main ran into the penalty area to take a lovely through ball from Billy Koumetio only for his first touch to let him down.
Larkeche picked up a loose ball and smashed a ferocious rising shot just past the post from 20 yards.
But two minutes later Dundee took the lead with a clever goal, great play between Larkeche and Cameron and Ziyad Larkeche raced into the box to score with a low drive which wemt in off the post.
It was what Dundee deserved, with Killie have a few break away which Dundee defended with ease.
The game turned on a refereeing decision after 43 minutes. Mo Sylla picked up a second yellow card in circumstances that puzzled the Dundee fans in the stands.
At half time Scott Fraser came on for the unfortunate Curtis Main to rebalance the midfield. Dundee had a few early chances which they failed to take. Kilmarnock did take control of the game as Dundee were pulled wide all the time.
Kilmarnock came close a few times and hit the post in one attack. Midway through the half Dundee replaced the hard-working Simon Murray and Scott Tiffoney with Seb Palmer-Houlden and Seun Adewumi to try and provide fresh legs that would give Killie more problems.
Dundee went 2-0 up on 81 minutes when a Palmer-Houlden knock on fell to Seun Adewumi who held off the defender to lob the ball home for a superb goal. It looked to win the games for Dundee.
But Killie pulled a goal back with 86 minutes gone, they levelled the game two minutes later. Then 4 minutes into injury time the scored the winner after Dundee failed to clear.
Dundee: McCracken. Portales, Clark Robertson, Koumetio, Ingram (Astley 88), Cameron, Sylla, Tiffoney (Adewumi 66), Larkeche, Murray (c) (Palmer-Houlden 66), Main (Fraser at half time). Unused Subs: Carson (gk), Mulligan, Fin Robertson, Braybrooke, Vetro.
Referee: Grant Irvine
Att: 5,316.
A tough day for DFC fans today and thet team must defend better for the whole game, they played some good football when they had 11 players. The sending off changed the game and it looked very very poor from the referee.
But we move on and big two games coming up v Motherwell (away) and St Johnstone at home.