The Welsh side edged a tight contest at Thomond Park courtesy of Dan Biggar's boot and a second half Rhys Webb try that keeps them at the summit of the table.
Munster, who were last defeated at home by the Ospreys in April 2010, took an early lead through centre Danny Barnes but Holley's side responded to clinch their sixth straight league win.
"It's one of the most difficult places to win in the league, so it's a result we can be pleased about," said Holley.
"Munster expect to win every home game, and their record suggests rightly so, but we were able to upset them thanks to a great team effort.
"We certainly won't become complacent. We realise that we've won nothing at this stage of the season and if we don't continue striving to improve then the hard work of the last six weeks could be wasted."
Despite winning at last season's champions, Holley is still adamant there is room for improvement, a scary thought for the rest of the RaboDirect PRO12.
He added:"It wasn't the perfect performance, we know that and we've made sure that the players understand it, but we can be justifiably pleased to have won this game.
"We probably should have scored more points in the first half but we were a little bit untidy, we weren't clinical enough, which meant we gave up possession at some key times.
"I think it was a bit of a smash and grab job with that wonderfully executed try the difference. We pride ourselves on our defensive work and that shone through in the closing stages when the team dug in for each other."
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