The defeat brought an end to the Gunners’ 100% home winning record this season, one they came very close to maintaining.
Munster, who are now in pole position for the Celtic League title, bounced back from their defeat to Irish rivals Leinster to dent Edinburgh’s hopes of leap-frogging them to the top of the table.
Munster announced their attacking intentions by turning down a shot at the posts with an early penalty and their initiative soon brought rewards.
Scrum-half Peter Stringer took a quick tap to spark a move that saw centre Trevor Halstead break the line and cross for the opening try. Flyhalf Ronan O’Gara added the extras.
The task facing the hosts got tougher when prop Dave Hewett was yellow carded shortly afterwards but Munster failed to capitalise in his absence.
O’Gara stretched their advantage when Hewett again was guilty of an infringement but the Gunners rallied with a try from experienced lock Scott Murray who burrowed his way over from short range.
Chris Paterson then closed the gap even further with a difficult conversion but O’Gara ended the scoring in the half with his second penalty.
Edinburgh continued to raise their game in the second half and the went close when the bounce went against winger Francisco Leonelli.
Halstead took centre stage again soon after for Munster, playing a key role in a move that saw winger John Kelly touching down for the score with an excellent finish.
Again the hosts rallied when Marcus Di Rollo intercepted a wayward O’Gara pass before racing away to score. Paterson’s conversion ensured a nail-biting finish.
A further late penalty from Paterson brought them to within one point but time eventually prevented them from stealing anything more than a losing bonus point.