The Borders took the lead with a penalty from flyhalf Charlie Hore and they were quick to build on their lead with a brace of tries. Stephen Cranston, returning from injury, grabbed the first sliding in after some great work from prop Tom McGee and lock Mark Blair.
Soon following over the whitewash was winger Simon Danielli who pounced for an interception and subsequently raced the length of the field to score. Hore added the extras on both occasions.
Hore stretched the lead to 20 points with another penalty but Munster showed they can nver be written off with their first try from Paul Devlin, converted by Jason Holland.
But the odds looked to be stacking up against the visitors when prop John Hayes was yellow carded before halftime as Welsh referee Phil Fear finally lost his patience after a string of rucking offences. Hore added three more to his own tally to leave his side well in control going into the break.
It was a different Munster side that emerged after half-time.
Hooker Gerry Flannery exploited some space to grab Munster's second try and Donnacha O Callaghan soon claimed the second after getting on the end of a powerful drive. When Holland added the extras the deficti was down to just four points.
Substitute centre Conan Doyle was the next to grab a five pointer and with the conversion from Holland the game had swung the Irishmen's way.
To turn the comeback into a rout Rob Henderson skipped in for the next score and veteran Anthony Foley crashed over with Holland once again adding the conversion.
Borders (23) 23 Tries: Cranston, Danielli Cons: Hore 2 Pens: Hore 3
Munster (7) 38 Tries: Devlin, Flannery, O'Callaghan, Doyle, Henderson, Foley Cons: Holland 4
Moffat, Danielli, Cranston, Pattison, Walker, Hore, Cusiter, McGee, Ford, Douglas, Blair, Stewart, McEntee, Miller, Brown.
Replacements: Morton for Cranston (68), Cross for McGee (63), Scott for Ford (64), Dalziel for Blair (53). Not Used: Kay, McKearchar, Warnock.
Payne, Kelly, Devlin, Henderson, Horgan, Holland, F. Murphy, Horan, Flannery, J. Hayes, O'Callaghan, O'Connell, Keogh, Wallace, Foley.
Replacements: Mullins for Payne (57), Doyle for Henderson (73), Stringer for F. Murphy (60), F. Sheahan for Flannery (65), Hogan for O'Connell (73), Quinlan for Keogh (60). Not Used: McGovern.