A stodgy encounter appeared destined to end in stalemate until 20-year-old Jaze Kabia, a January capture from Shelbourne, notched his first-ever goal for the Lions after 87 minutes.
With Killie rattled, the tireless Scott Pittman, celebrating his 250th outing for the club, almost immediately rippled the net to make the points safe.
The result – which could have been more handsome, given Jon Guthrie struck the bar in the first half – sees the West Lothian outfit move to within five points of fourth-placed Hibernian with a game in hand.
David Martindale, deemed a fit and proper person by the Scottish FA following a hearing on Tuesday, remains yet to taste defeat since succeeding Gary Holt last November and has overseen 10 wins and two draws.
He made four changes to the side that defeated St Mirren to reach the Betfred Cup final. Gavin Reilly made his first start for the Lions and Jack Fitzwater, Ciaron Brown and Alan Forrest were all drafted in. Hampden goal hero Scott Robinson, Craig Sibbald, Efe Ambrose and Julien Serrano dropped out.
Killie, back in action after an 11-day hiatus, handed a debut to new signing George Oakley.
It was in-form Livi that made the early running, with Forrest forcing a fine finger-tip save from Danny Rogers after scampering in behind full-back Aaron McGowan.
The hosts came even closer to breaking the deadlock when Guthrie, who boasts five goals already this term, once again illustrated his threat by heading a Josh Mullin corner against the bar.
Kilmarnock awoke from their slumber after the interval, with Chris Burke forcing a comfortable low stop from Livi number one Max Stryjek and Oakley fizzing an instinctive drive over the bar from a tight angle.
However, it would be Livingston who snatched the spoils during a breathless finale.
Kabia, thrown on as a late substitute, reacted swiftest to a blocked Sibbald shot and produced a low drive which found the roof of the net via a slight deflection off Ross Millen.
And Pittman marked his milestone appearance by finding the net, haring onto a hopeful ball forward and poking an effort beyond Rogers.