Having led 16-3 early in the second half, Clermont were forced to hang on amid a spirited and gutsy Munster revival.
And Cotter believes that is a crucial lesson for his players as they chase a domestic and European double this season.
"The most important thing is that we are delighted to have won and reached a final," he said.
"Moments like that are for the players. They are the ones who experience those fantastic moments on the pitch, I'm just hear to guide them and if we are to be the best team in Europe then I will be very happy.
"But we also learned a lot today against Munster, they never gave up and were very committed. Experience is important in sport and we will use this for the next game.
"We have three weeks to prepare for the final which is very important. We will analyse the game and then move on. We still have another Top14 game next week which is very important because it is also our last home game of the season.
"Then we can look forward to returning to Dublin."
Clermont have already enjoyed success at the Aviva Stadium - the venue for the 18th tournament final on Saturday, 18 May - after beating 2012 Heineken Cup champions Leinster 28-21 there in December.
And they accounted for another Irish side after Napolioni Nalaga's early try and the trusty left boot of Morgan Parra.
Cotter said: "Initially in the first half we managed to prevent Munster winning possession. We knew they wanted to have a really big scrum and try to walk all over us in the driving mauls but we showed from the start that it was going to be a very physical match.
"But there was a critical moment before half-time when we were trapped on our own five-metre line. At that point in the game you are getting tired and not so lucid and the game could have turned against us but we knew how to defend and managed to keep them out. Defence is a team character and we showed that again here.
"Munster changed their approach in the second half and started kicking long but I'm really proud of the way our players really adapted to that quickly."