In the end, it was Cotter's opposite number Conor O'Shea who was able to look back on a bonus point after outside half Nick Evans dropped a goal in the 82nd minute to get his team within seven points to secure a priceless point.
"You have to be happy with a win, especially against the Harlequins. They had lost at home last and came here knowing the importance of the game. If they had got a result here the Pool would have been wide open again," admitted Cotter.
"We took four points and I was pleased we scored three tries. Yes, I wish we had scored one more, but they are a good team. We'll take that and keep moving forward."
The win brought Clermont back in the hunt in Pool 4 and set them up for a classic set of games in December against the Scarlets. The Welsh region's 26-26 home draw against Racing Metro kept them on top of the Pool, but with only one point difference between the top three teams it looks like being a tense finish to the Pool.
"I'm probably happier than disappointed. We're always going to look at how we could have done things better, especially in the second half, but we'll take the win for now," said Cotter when asked about the bonus point.
"We scored three well created tries, played some good rugby, but we are still missing something. We have to keep working on keeping the pace up throughout the whole game. We played wide in the first half, then maybe a closer game in the second, without being rewarded."