Clarke left out Long against his former club but he came off the bench to tee up the second-half winner for on loan Chelsea striker Romelu Lukaku.
Clarke said: "Shane has been terrific for me this season and it was a difficult decision to leave him out.
"I just thought Lukaku had been very patient waiting for his chance from the bench.
"I also felt I was always asking Shane to do the horrible shift which is the first hour, where he runs and chases and defenders are still fresh.
"I thought it would benefit Shane to go on as the fresh player for a change and thankfully for me and the team, it worked."