Dundalk lost their lead twice in Derry as Declan Devine's men fought back from Daniel Kelly and Daniel Cleary goals - Darren McAuley's 83rd minute equaliser the normal-time highlight at the Ryan McBride Brandywell.
But a Georgie Kelly winner in the 117th minute ensured that Vinny Perth's side left Derry with a place in the last eight.
Harry Kenny's St. Pat's side were left shell-shocked tonight as Premier Division strugglers UCD hit three past them in an impressive comeback as they marched into the FAI Cup quarter-finals.
The Saints found themselves two down at the break thanks to goals from Liam Kerrigan and Yousef Mahdy before Kerrigan struck again to make it three. Conor Clifford found the net late on, but it proved a mere consolation.
There was drama at Dalymount as Bohemians were let off the hook as Sam Verdon missed a late penalty to send Longford Town through.
Andre Wright put Keith Long's men in the opening moments of extra-time, but that was short-lived as Jack Doherty pulled one back minutes later. It went to penalties and James Talbot was the hero for Bohs as he saved opposite goalkeeper Lee Steacy's spot kick in sudden death.
Elsewhere, Shamrock Rovers were comfortable as four second-half goals sent them past Drogheda United into the last eight.
Galway United are into the quarter-final and were full value for their 1-0 win over Cork City out west - with Conor Melody's first-half header the only goal.
Donegal lower-league side Glengad United host Waterford and Sligo Rovers host Limerick tomorrow while Leinster Senior League heavyweights Lucan United and Crumlin United clash on Sunday to complete the quarter-final line-up.
Results
Derry City 3-2 Dundalk (AET)
UCD 3-1 St. Pat's
Shamrock Rovers 4-0 Drogheda United
Galway United 1-0 Cork City
Bohemians 1-1 Longford Town (5-4 PENS)
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