The hosts left the possibility of qualification behind them with a sluggish show against a physically superior London Scottish side that fully deserved victory.
Yet, despite taking the win and overtaking Munster to secure second place in the pool, the exiles side failed to make it to the knock-out stages by just a single point.
Remarkably, Moseley, runners up to Leinster in Pool 1, and hammered twice by the Irish side, advance. Munster A head coach Mick O’Driscoll did little to hide his frustrations.
“This is very disappointing. We were very poor in the first-half and it killed us, to come in 5-3 down at half time with a wind like that at our backs was always going to make it very difficult for us. We were struggling after that first-half when we were really non-existant.”
Johnny Holland kicked an early penalty but Munster were unable to use the wind to their advantage. They struggled to win primary possession and had to face a hugely determined London Scottish defence when they did.
A 34th minute try from skipper Mark Bright gave the visitors the lead and a significant boost.
Munster responded vigorously in the second-half and played considerably better.
Holland restored the lead with his second penalty after 57 minutes but Peter Lydon hit back with two excellent penalties and converted a clinching 70th minute try from Jason Harries.
Cian Bohane’s brilliant try gave Munster hope but London Scottish were in no mood to give up the advantage and Lydon kicked a late penalty to seal the win.
Leinster A are the only Irish province to advance to the last eight of the competition.
Leinster A v Moseley, Yorkshire Carnegie v London Welsh, Bedford v Jersey, Cornish Pirates v Doncaster.
D Johnston; S Fitzgerald, D Goggin, C Bohane, D Sweetnam; J Holland, D Williams; L O’Connor, K O’Byrne, P McCabe; L Nicholas, S McCarthy; J Coghlan, S Doyle, S Buckley (captain).
C Oliver for Doyle (40), J Poland for Foley (48), B Scott for McCabe (70), N Hodson for Goggin, S McMahon for Fitzgerald (both 74), E Rossiter for O’Byrne, O Lyons for Coghlan (both 79).
P Lydon; A Turner, J Harries, C Jackson, R Weir; L Millar, G Horne; K Schonert, D Cherry, M Maidment; R Bartle, J Thomas Brown; A Brown, T du Plessis, M Bright (captain).
J Gibbons for Schonert, M Shields for Maidment (both 40), A Kwasnicki for Cherry (49), N Earle for Horne, T Moran for Browne (both 64), W Carrick-Smith for du Plessis (68), M Heeks for Harries (77).
C Ridley (England).