Paul O'Connell returned to the Munster squad after injury
Edinburgh: (9) 9
Pens: Godman 3
Munster: (16) 35
Munster retain hopes of finishing in the top four of the Magners League as they ended Edinburgh's hopes of being Scotland's top finishers.
Tries: O'Connell, Quinlan, Fogarty
Con: O'Gara 3
Pens: O'Gara 3
Ronan O'Gara converted an early penalty try for the Irish side before Phil Godman replied with two penalties.
Two O'Gara kicks and one from Godman had Edinburgh in touch at half-time.
But Munster ran away with victory thanks to tries by Paul O'Connell, Alan Quinlan and Denis Fogarty put and further kicks from O'Gara.
Edinburgh's hopes of beating Glasgow to becoming Scotland's top seeds in the Heineken Cup are now lost with one game remaining.
Munster are equal on points with Glasgow and a point behind Ulster. The home side had been dealt an instant blow when the Irishmen were handed a controversial seven points from a penalty try.
Edinburgh's players and fans could only shake their heads in disbelief as Welsh referee Phil Fear ruled they had deliberately hauled down a maul close to the line.
O'Gara's conversion from dead in front was a formality.
Edinburgh shook off the setback to battle their way back into the contest thanks to two penalties in quick succession by stand-off Godman.
But O'Gara fired one over at the other end to grab back the momentum for the visitors - and he repeated the feat to give his side more breathing space.
Godman completed his penalty treble to give the Gunners fresh hope in the build-up to the interval.
However, there was enough time for O'Gara to notch his own hat-trick with Scotland star Simon Taylor in the sin-bin.
Any prospect of an Edinburgh fightback was snuffed out with a Paul O'Connell try, goaled by dead-eye O'Gara.
Further Munster efforts came from Alan Quinlan and Denis Fogarty.
Edinburgh: Lopez Fleming, Dewey, Cairns, Dey, Webster, Godman, Laidlaw, Jacobsen, Kelly, G. Cross, Strokosch, Murray, Taylor, MacDonald, Hogg.
Replacements: Rennie for Webster (71), Hodge for Godman (46), Senio for Laidlaw (64), Hall for Kelly (59), Dickinson for G. Cross (40), Pringle for Strokosch (56), S. Cross for MacDonald (64).
Munster: Carney, Horgan, Murphy, Mafi, Dowling, O'Gara, O'Leary, Pucciariello, Sheahan, Buckley, O'Connell, O'Driscoll, Quinlan, O'Sullivan, Foley.
Replacements: O'Meara for O'Leary (74), Roche for Pucciariello (74), Fogarty for Sheahan (69), Lawlor for O'Sullivan (40), Leamy for Foley (61). Not Used: Wallace, Manning.
Ref: Phil Fear (WRU)