However, Flannery - a British and Irish Lions tourist in South Africa last year - and his teammates slipped to a 16-15 defeat and their chances of finishing top of the league now look slim.
Northampton are next up for Munster and Flannery said: "It is a setback. Generally, we've always managed to pull out a big league win coming into big Heineken Cup matches.
"We've lost and we have to look beyond that. At least it was a really intense game; we could have had a game with no intensity.
"Defences will probably come out on top next week, but we need to be more smarter, more streetwise and sort out the discipline.
"We've just been as affected by international disruptions as Northampton and Leinster. It's a matter of jumping the gun ahead of them.
"You've always next week to redeem yourself in rugby, that's the beauty of it. We can't feel sorry for ourselves."