The Blues lost 16-13 to the double European kings and three-time Celtic champions at Thomond Park.
Trailing 16-3 at half time, the Blues produced a superb performance in the second 40 minutes but ultimately fell just short in Limerick.
A Dan Parks penalty handed the Blues an early lead before Munster took control with a Felix Jones try handing the hosts the initiative with just over a quarter of an hour played.
The young full back, who was making his first home appearance since injury ruled him out of the World Cup, raced in underneath the posts after a fine burst from wing Simon Zebo.
Former Connacht fly-half Ian Keatley added the conversion having slotted a 10th-minute penalty to push Munster 10-3 clear.
Keatley, who was deputising for veteran playmaker and Ireland squad member Ronan O’Gara, struck two further penalties in quick success on 21 and 23 minutes to leave the Blues with a mountain to climb in the final hour or so.
But Gareth Baber and Justin Burnell’s troops refused to buckle when the Munster support began to except a whitewash. Instead of giving up the ghost after such a disappointing start, the Blues hit back after the interval.
Wing Richard Mustoe started the fightback eight minutes in as he finished off a flowing move that began with an impressive midfield burst from Gavin Henson.
Parks slotted the testing conversion and suddenly the Blues were back within a single score at 16-10.
Keatley and Parks both missed three-point opportunities before replacement full back Ben Blair brought the Blues even closer with 15 minutes remaining.
The Blues’ hopes of a famous triumph were dealt a serious blow five minutes later, though, as second row and skipper Paul Tito was sent to the sin bin. The New Zealander saw yellow for killing the ball but the Blues kept Munster scoreless during his 10 minutes off the field.
Thomond Park lacked its usual air of confidence in the closing stages as the Blues pressed for more than just a losing bonus point but a final score evaded the visitors.
The result sees the Blues drop to sixth in the standings while Munster moved to within a point of the second-placed Ospreys.
