The Scottish capital outfit had only won once in four attempts all season whereas Munster went into the clash sitting top of the table and on a winning run that stretched to 14 games.
While the Munster line-up showed 10 changes from the side that defeated Cardiff Blues the week before, and half the squad was aged 24 or under, coach Tony McGahan would have hoped for better from his side who found themselves 16 points down at the end of the first quarter.
Following three Greig Laidlaw penalties, centre Matt Scott celebrated his 21st birthday in style with the game's first try.
Munster finally woke from their slumber and fly-half Ian Keatley landed three penalty kicks at goal to reduce the deficit to seven points at the interval.
Edinburgh, though, came out with renewed energy at the re-start and Laidlaw supplied his fourth penalty before hooker Steven Lawrie crashed over for a try. Laidlaw added the extras to take the score to 26-9 in the home side's favour.
Defences stayed on top until Danny Barnes pulled five points back with a try for Munster following a well-worked backs move; however Edinburgh skipper Laidlaw appropriately had the final say with a fifth penalty to take his personal contribution for the match to 19 points.
The victory was only Edinburgh's second against Munster in the last 10 meetings between the sides.