Albion arrived at the Liberty Stadium on the back of four straight wins which had lifted them to third in the Premier League, but a superb display from the home side saw them power 3-0 ahead inside 40 minutes.
Romelu Lukaku pulled a goal back in first-half stoppage time to prompt a distinct improvement from the Baggies after the break, but they were unable to breach a disciplined Swans defence again.
"If we had got it to 3-2 it may have been different but we didn't and I can sit here and say we deserved to lose," said Clarke.
"The players put themselves in a hole and in the second half I challenged them to get out of the situation and to be fair they did that.
"We had a chat about what we did wrong, and what we needed to do better and they did do better.
"The players know, and our fans are knowledgeable enough to know, it is a tough league and you will have days like this and I am looking forward to Saturday to see a response.
"Of course we want to bounce back, we didn't play well in the first 45 minutes but we responded at half-time, that is football - some games you win, some you lose - but we move on."