At one stage in the second half Munster led the Italians by 10 points after Ireland prop Stephen Archer crossed for just his second ever try for the province and Ian Keatley converted.
However, Archer later went on to pick up a yellow card eight minutes from time, joining Niall Ronan, Duncan Williams and Cathal Sheridan as the players to earn a ten-minute timeout.
Two tries from flying winger Ludovico Nitoglia gave Benetton Treviso their first win of the season, making it two victories on the trot over Munster at this venue - the Reds were beaten 34-10 on their last visit back in February.
It had all started so well for Rob Penney's side on a night when Peter O'Mahony returned to take on his official duties as Munster's captain for the season.
Despite Keatley missing a tricky penalty early on, Munster raced into a 5-0 lead when seasonal debutants Simon Zebo and Keith Earls linked up for the latter to score down the right flank - the groundwork for the try being laid by centres Casey Laulala and James Downey.
Keatley was unable to add the conversion and five minutes later former Leinster out-half Mat Berquist got Treviso off the mark with a penalty.
Moments later Ronan was shown a yellow card by referee Leighton Hodges, but worse was to follow when Berquist gave Treviso the lead by slotting the resulting penalty.
Penney would have been delighted to not see a further impact on the scoreboard while his team were down to 14 men. With their openside flanker back on the pitch, Munster began to improve.
After a series of powerful scrums under the posts that produced three penalties, Hodges eventually awarded Munster apenalty try that their scrum domination deserved, giving them a 12-6 lead after 26 minutes.
But the home side hung in there and four minutes from the break Berquist was on target once again with a penalty awarded after Billy Holland failed to roll away from a ruck.
Munster led 12-9 at half-time and that advantage was increased in the 46th minute when Archer got on the back of a powerful rolling maul and Keatley slotted the tricky conversion to give the league leaders a ten-point cushion.
But that was as good as it got for Munster as Nitoglia touched down twice in a 12-minute spell for Treviso to turn the game on its head.
Either side of his second try, Berquist picked off penalties to give Treviso a crucial ten-point cushion and with Williams, Sheridan and Archer also seeing yellow, Munster had little hope of mounting a comeback as their Italian adventure ended on a losing note.
Giving his reaction afterwards, Munster boss Penney said: "We've just taken a massive step backwards. You can't afford to lose four players, as we did over the course of 80 minutes, and hope to get away with it."