Munster (7) 12
Tries: Jones, Howlett
Harlequins (14) 20
Tries: Robson, Care
Conversions: Evans, Care Penalties: Clegg 2
Gonzalo Camacho was a livewire on the left wing for Quins
Harlequins pulled off one of their most famous wins with a stirring defeat of Munster in the semi-final of the European Challenge Cup.
Quins were rampant in the first half, tries from George Robson and Danny Care taking them into a deserved lead before a Felix Jones try pegged them back.
Fly-half Rory Clegg made it 20-7 with two penalties after the restart.
And despite Nick Easter's late sending-off and Howlett's try giving the hosts hope, Quins deservedly held on.
It was only the second time Munster had been beaten at Thomond Park in 42 European encounters - Leicester were the only previous victors in 2007 - and the first time this season.
Quins started the match at break-neck speed, a huge hit by Maurie Fa'asavalu on Keith Earls setting the tone for the first half an hour, and the home faithful were stunned into virtual silence at times as Munster were hit by wave upon wave of attacks.
And the visitors finally breached Munster's defence in the ninth minute when wing Gonzalo Camacho went on a snaking run down the left flank, leaving Paul Warwick and Howlett in his wake, before the ball went right and lock Robson rumbled over in the corner.
After Quins fly-half Nick Evans had kicked the extras, the visitors did not let up, their swarming, offloading game creating havoc in the opposition defence.
First, Evans almost put Ugo Monye in with a clever kick over the top before Mike Brown was held up over the line. Ronan O'Gara was forced into a try-saving tackle on George Lowe.
Having made 50 tackles in the first 15 minutes Munster finally made it into Quins' 22 in the 17th minute when number eight James Coughlan seized on an errant tap-back at the line-out, only to be foiled by some terrific scramble defence.
With Munster's line-out in tatters, muscular Samoan flanker Fa'asavalu made hay, pouncing on loose ball after loose ball before barrelling through tackles seemingly at will.
When Evans missed two very kickable penalties it seemed as though Munster might have partially weathered the storm, only for scrum-half Care to wriggle over and slot the conversion to make it 14-0.
However, as half-time approached there was a sense the visitors had not made the most of all their possession, and that proved to be the case.
I'm incredibly proud. The guys will have today's win in their locker forever and a day
O'Gara kicked for the corner when his side could have taken three points and from the resulting line-out the ball was shipped right and Jones breezed over in the corner unopposed.
As expected, Munster came flying out of the traps in the second half and Paul O'Connell - on as a replacement - immediately made his presence felt with two soaring takes at the line-out.
But it was Quins who struck first after the break, Clegg, on for the injured Evans, slotting a penalty to make it 17-7.
Clegg then offloaded to Jordan Turner-Hall, who went crashing through the Munster midfield, only for the move to break down when Care's floated pass to Camacho was intercepted by Denis Leamy.
Clegg extended Munster's lead with a penalty from bang in front on 58 minutes before Lowe was disallowed a possible penalty try. The Quins centre was involved in a foot race with Warwick and Howlett and appeared to be impeded, but the video referee ruled out any foul play.
Referee Romain Poite then made two potential match-deciding decisions, both of them correct.
First, Howlett went over in the corner, only for Jones' pass to be ruled forward; second, Howlett was called back after O'Connell's offload was also ruled forward.
The incensed home crowd spurred their side to new heights and the upshot was the sending-off of Easter, who received a second yellow card for coming in at the side after some desperate defending.
Howlett very nearly unlocked Quins' defence again when he hunted down a chip and chase, but Brown was there to cover.
The former All Black did finally give Munster hope with two minutes remaining with his side's second try but, unfortunately for the hosts, O'Gara missed the conversion which left them requiring two scores, and the English side held firm.
Conor O'Shea's side will play Stade Francais in the final on 20 May in Cardiff, where Quins will be hoping to add to their victories in 2001 and 2004.
Harlequins director of rugby Conor O'Shea:
"We might not have the squad size that a lot of teams have but we have a hell of a lot of heart. I'm incredibly proud, as you can imagine for various different reasons.
"But the horrible thing is that we have done nothing. We have won a semi-final.
"My dad has a saying that a good semi-final never makes a good final, so we're going to have to make sure that that doesn't happen. But the guys will have today's win in their locker forever and a day."
Munster head coach Tony McGahan:
"The way that we played didn't give us any opportunity whatsoever to get a result.
"We really stood off them, and showed an inability to make first-up tackles. I don't think we got through more than two phases in the first half, and we conceded 11 turnovers. We failed to put any doubts in their mind.
"If they show the same spirit and execution that they showed today, then I don't think they will have any problems."
Munster: Jones; Howlett, Mafi, Warwick, Earls; O'Gara, Murray; du Preez, Varley, Buckley; O'Callaghan, O'Driscoll; Leamy, Wallace, Coughlan.
Replacements: O'Connell for O'Driscoll (40), Hayes for Buckley (40), Tuitupou for Warwick (40), Horan for du Preez (57), Stringer for Murray (57), J Murphy for Mafi (65), D Ryan for O'Callaghan (68), Sherry for Varley (74).
Sin Bin: O'Callaghan (47).
Harlequins: Brown; Camacho, Lowe, Turner-Hall, Monye; Evans, Care; Marler, Gray, Johnston; Kohn, Robson; Fa'asavalu, Robshaw, Easter.
Replacements: Clegg for Evans (40), Jones for Marler (66), Vallejos for Kohn (73).
Not Used: Cairns, Lambert, Skinner, Moore, Chisholm.
Sin Bin: Easter (47).
Sent Off: Easter (70).
Ref: Romain Poite (France).