Goals from Jason Scotland, Darian MacKinnon and substitute Nigel Hasselbaink were enough to secure the points for Martin Canning’s men despite having to come from behind in Ayrshire.
Lee Ashcroft and substitute Greg Kiltie struck for Kilmarnock either side of a fine Accies comeback, in an entertaining game.
However, defeat leaves the hosts still nervously hovering just above the play-off spot.
Kilmarnock looked to apply pressure early on and broke the deadlock after just eight minutes when Ashcroft rose highest to bullet home a header from a corner.
Alexei Eremenko thought he had doubled his side’s lead just a minute later after coolly getting on the end of a 40-yard pass but he was flagged for offside.
Accies started to enjoy more of the ball as the first half wore on with Michael Devlin heading just wide from an Alister Crawford corner.
The visitors got their equaliser after 24 minutes when Louis Longridge’s effort was blocked by Craig Samson but Scotland was on hand to follow up and slam the ball into the net.
Hamilton thought they had scored again two minutes later but Darian MacKinnon was ruled offside.
Longridge then went close twice in quick succession but was denied on both occasions by Samson.
Josh Magennis then had a great chance to restore his side’s lead after breaking through one-on-one with Michael McGovern in the Hamilton goal but the keeper blocked well.
Dougie Imrie forced Samson into another good save just before the hour mark when his powerful run and shot was beaten away by the Killie keeper.
However, Accies did take the lead shortly after when Longridge’s cross was deflected into the path of MacKinnon on the edge of the box who fired into the bottom left hand corner.
Substitute Nigel Hasselbaink made it 3-1 just two minutes after coming on when he latched on to a through ball from Crawford, with his finish just squirming under Samson and over the line.
However, Killie were handed a lifeline when their own supersub Kiltie guided his effort into the net from just inside the box to set up an exciting final 10 minutes.
Manuel Pascali almost salvaged a point for Killie but his header came back off the post as the hosts pushed for an equaliser.
In the dying minutes referee Steven McLean had to separate a melee on the pitch with Ashcroft and Hasslebaink both finding their way into his book following a heated exchange.