Pat Hoban broke Bohs hearts from the spot deep in injury time - and for the second time in five weeks at Oriel Park.
Dundalk hitman Hoban struck home in the 95th minute to make it three wins from three against Bohs in just 35 days - and after the Gypsies had fought so bravely with 10 men for most of the second half for a point.
It will go down as the night of five substitutes. Bohs had one sub - Ryan Graydon - sent off and another hauled off - Ali Reghba - in this meeting of second versus third.
Gypsies boss Keith Long intervened to prevent Bohs going down to nine men in the final quarter as the youngster was quickly booked before committing a couple more fouls.
In between, livewire Dundalk replacement Georgie Kelly brought his side level and then, with time almost up, Scott Allardice - who was Bohs' replacement for Reghba - pulled down the Lilywhites' last sub Dean Jarvis in the box.
Up stepped Hoban and his goal prevented Dundalk from losing ground to Shamrock Rovers. For a long time, and despite so much pressure, it looked like Bohs would cling on as the hosts lacked a ruthless edge.
Credit was also due to James Talbot in the Gypsies goal and to Darragh Leahy and Andy Lyons for goal-saving clearances, but Dundalk found a way in the end.
Having kept Bohs scoreless in the two recent victories, the hosts coughed up a goal after less than two minutes.
Dundalk were rueing a half chance missed when they were caught cold on the counter, as Bohs swiftly turned last-gasp defence into scintillating attack.
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Robbie McCourt bypassed the home defence and Gary Rogers was slow to react as Danny Grant fired home from a tight angle.
Dundalk had a great opportunity to restore parity in the sixth minute when Sean Gannon's centre was met by Daniel Kelly, but he ex-Bohs man's first-time shot was tipped over by James Talbot.
Michael Duffy should have equalised in the 17th minute when he was teed up by Patrick McEleney, but he miscued wide.
At the other end, Danny Mandriou had a shot deflected for a corner.
Dundalk kept coming but Daniel Cleary's looping volley drifted wide before Jordan Flores' piledriver looked destined for the net - only to strike Hoban and go out for a goal kick.
Bohs lost Grant to injury in the 40th minute, with Graydon replacing him. When Gannon mis-controlled a Graydon pass on the edge of his own box, Swan snatched at his shot.
The hosts pressed hard from the start of the second half and, from a Flores corner, Cleary blazed over.
Graydon's second booking for a foul on Cleary saw him deservedly dismissed and Dundalk looked to capitalise quickly.
Kelly was replaced by his namesake Georgie but Leahy brilliantly denied the new arrival twice from close range on the hour. Soon after, Kelly had a header saved by Talbot.
Flores made way for Sean Murray on 65 minutes and, within 90 seconds, the pressure told as Kelly pounced on the loose ball from a corner to drill home.
Dundalk attacked in waves but chances came and went, with Talbot superbly denying Hoban on 87 minutes and Lyons somehow keeping Cleary's effort out.
But in the end Dundalk weren't to be denied as the Lilywhites faithful acclaimed the late winner.
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