The Irish region, currently third in the RaboDirect PRO12, lost their 17-game unbeaten European streak as well as ground on the French side at the top of Pool Five.
And although they prevented Clermont from scoring a try of their own, the accurate boot of Morgan Parra and a drop goal from Brock James helped the hosts extend their winning home record to 51 games.
But after fly-half Jonathan Sexton's first-half penalty miss came back to haunt his side, Schmidt insists raising spirits ahead of the return fixture next week will be difficult.
"It is incredibly disappointing. The fact that we've got to try to get ourselves up and forge ahead for next week is going to be tough as well," said Schmidt. "We've got a fair few bruised bodies in there.
"I just think you come to the (Stade) Marcel Michelin and I think you've got to get over the line. You can't just go between the posts and hope to get something here.
"I thought there were a couple of calls that maybe could have gone our way and we could have got something else between the posts.
"But the area that Jonny actually kicked out of when he cross-kicked was very, very heavy and muddy. It's not a guaranteed three.
"We did miss one and they didn't miss any. So that's how close these games are and it is really unfortunate."
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