Clarke left out out Long against his former club but he came off the bench to tee up the second half winner for on loan Chelsea striker Lukaku.
Victory lifted Baggies into third spot in the Barclays Premier League with 10 points from their opening five games.
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."
Lukaku had also scored as a substitute in the 3-0 win over Liverpool and Clarke is aware he could return to Stamford Bridge in January if he maintains his fine form.
He said: "Lukaku is here on a season-long loan but I would imagine there is a recall clause in the agreement.
"Any Premier League team who does a season-long loan usually has a January release clause.
"There's no point in worrying about things I can't affect. I'm just looking for Romelu to continue the fine form he's shown for us and score a few more goals.
"If he scores 20 goals by Christmas and and Chelsea want him back there's nothing I can do about it.
"He had a number of clubs he could have gone to, we're just thankful he's come here to the Albion."
Clarke has played down Albion's flying start to the campaign.
He said: "Third in the table doesn't mean anything. Our aspirations are the same.
"The only aspiration I have at this time is getting another team together for Wednesday night (against Liverpool) in the Capital Cup, which we look forward to.
"We also have another difficult league game to look forward to next week against Aston Villa. We go from game to game.
"For now the primary objective for 75% of the Premier League is to get to the margin of points to keep you safe."
Reading are still searching for their first league win and Royals boss Brian McDermott stressed the need for unity.
He said: "It was frustrating. We spoke at half-time and said whatever happens keep a clean sheet and the goal was disappointing from our point of view.
"You never want to be bottom of any league. All we can do is stick together and we've done that.
"We have to make sure everyone is right for the next game and that's what I'm confident will happen.
"This is an unforgiving league. We know that. It is fantastic to play in and we want to be part of that.
"We were bottom of the Championship at one stage last season and ended up winning it.
"We did exactly what we did now, we have to stick together."