Leicester Tigers wing Murphy, who returns to Ireland with Munster next season, was brought into the starting line-up when Shane Horgan was ruled out by a stomach bug.
But tries by Xavier Rush, George Smith and Cedric Heymans, together with 11 points from Brock James and a penalty from Jean-Baptiste Elissalde, allowed the Barbarians to celebrate their first-ever victory at Thomond Park.
Ireland trailed 21-3 before half-time, but fought back with tries from Niall Ronan and Tony Buckley, while captain Ronan O'Gara kicked the hosts to within six points.
Leicester Tigers prop Julian White was among the Barbarians replacements after making his debut in the famous black-and-white hoops in the defeat by England on Sunday, while his former Leicester colleague Seru Rabeni also played his part.
Ireland: Rob Kearney; Johne Murphy, Gavin Duffy, Fergus McFadden, Andrew Trimble; Ronan O'Gara (c), Peter Stringer; Marcus Horan, Sean Cronin, Tony Buckley, Ed O'Donoghue, Dan Tuohy, John Muldoon, Niall Ronan, Chris Henry. Replacements: Donncha O’Callaghan for Ronan (30-36), Paddy Wallace for McFadden (41), Tommy Bowe for Kearney (54), Jerry Flannery for Cronin (55), Mick O’Driscoll for O’Donoghue (55), Donncha O’Callaghan for Tuohy (55), Tomas O’Leary for Stringer (62), Tom Court for Horan (65), Cronin for Flannery (80).
Barbarians: Paul Warwick, Cedric Heymans, Casey Laulala, Seru Rabeni, David Smith; Brock James, Pierre Mignoni; David Barnes, Schalk Brits, Census Johnston, Jerome Thion, Malcolm O'Kelly, Alan Quinlan, George Smith, Xavier Rush (c). Replacements: Julian White for Quinlan (36-46), White for Barnes (46), Byron Kelleher for Mignoni (50), Jean-Baptiste Elissalde for James (50), Rodney So’oialo for O’Kelly (52), Benoit August for Brits (52), Martyn Williams for Rush (62), Fabrice Estebanez for Rabeni (64), Barnes for Johnston (66), Johnston for White (68).