Edinburgh remained in contention at the interval with Munster leading just 6-0 but scrum-half Conor Murray and forwards Peter O'Mahony and Sean Dougall all went over in the second half.
Hooker Damien Varley crossed for the bonus-point try as the match was entering stoppage time after fly-half Ian Keatley had kicked 13 points.
Munster's attentions now turn back to the RaboDirect PRO12 with Zebre next up at Thomond Park on Friday - and Penney believes they are ready to take their European form back into the RaboDirect PRO12.
"There's light at the end of the tunnel and given another few months of this understanding, of us working together and having faith in each other, we'll be a better side and we'll continue to be a better side," Penney told the Irish Independent.
"I've explained to the lads when you are going through anything new as an athlete you end up in a dark place.
"It's a horrible place to be because it's so easy to go back and rely on what you used to be familiar with.
"But when you pop out of it the sun's a lot brighter and you can actually far exceed anything you were able to do previously.
"[In the first half] we just hadn't capitalised and got the rewards.
"We needed to improve on our ball security, our ability to capitalise on the space that's provided for us, and that space happened on about five or six occasions.
"We had really good intent and that was evident all week at training. There was an edge which you'd expect after the last few weeks.
"We created pressure which we hadn't been able to do consistently well. We didn't do it as well as we can but we did enough to squeeze Edinburgh.
"Conor played a good game last week and he's bounced back and had a terrific performance, error-free. Ian Keatley drove the team around the park more authoritatively."
Guinness PRO12 Munster News
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