Borders' hopes of giving coach Tony Gilbert a winning send-off were wrecked by Munster.
Borders (3) 10
Munster (15) 18
Tries: Horgan, Foley
Pens: Staunton (2)
It was also a sad exit for ex-Scotland hero Gary Armstrong, who was forced off with a first-half leg injury.
Munster had the match won at half-time after Anthony Horgan pounced on a turnover ball for a try and Anthony Foley was driven over for a second.
Borders' Ian Berthinussen bagged a fine second-half try to keep the contest alive but Munster held on for victory.
Borders: Morton, N. Walker, Berthinussen, Utterson, Cranston,
Vili, Armstrong, Cross, Scott, Douglas, Weir, Stewart, MacLeod,
Sititi, K. Brown.
Replacements: Ford, Johnston, Davidson, Dalziel, Fairley,
Munster: Cullen., Payne, Mullins, Holland, Horgan, Staunton,
Reddan, Horan, Flannery, J. Hayes, Pusey, O'Connell, Quinlan,
Replacements: Roche, McIlwham, Hogan, S. Keogh, Callaghan..,
Referee: Neil Ballard (WRFU)