Only a correct decision from the TMO prevented Wesley Fofana from claiming a match-winning score at the death and Cotter admits that coming so, so close is a bitter pill to swallow.
"It's disappointing, very disappointing. We put in so much effort and that wasn't rewarded," said Cotter, whose team were appearing in a first Heineken Cup semi-final against a side that have been in the last four.
"We'll need time to digest the defeat. It's very difficult to talk about it right now. It's a game that I don't want to watch again straight away but I'll have to.
"It was a very tough game, a very close game, but it's always like that in knockout games. We have to use it and learn from it to make sure we win next time.
"I thought it was try at the end when I saw the reaction of the players. But the ref went to the TMO and it wasn't given. We started again after that with our pick and go but we just couldn't score."
Clermont lost star backs Julien Malzieu and Lee Byrne to injury early on at the Stade Chaban Delmas but Cotter refused to use that misfortune as a reason for the narrow loss.
Instead the New Zealander focussed on a costly six-minute spell immediately after the break when Leinster turned a 12-6 deficit into a 16-12 lead thanks to a converted Cian Healy try and a Rob Kearney drop goal.
"The beginning of the second half was frustrating for us," added Cotter.
"We were six points ahead and they scored a try and a drop goal.
"We played against the wind in second half and we didn't adapt well. I'm disappointed about that.
"It wasn't planed for us to make so many changes so early but the bench know they need to be ready at any time and they did well. Maybe it was a little bit of a disruption but it wasn't that critical and I was happy with how Jean-Marcel Buttin and Regan King played.
"There are some very positive points to take from the game even if we are disappointed.
"The last few minutes showed the will, character and spirit of the team. Everybody agrees that this squad has character - now we have to work on some details."