The 19-year-old missed a spate of opportunities at St James' Park and, despite cancelling out Demba Ba's opener with a headed finish, the Belgian ended up on the losing side as Papiss Cisse struck late on.
However, though Clarke conceded that Long - who has three Premier League goals already this season - did not deserve to be benched, he underlined the selection headache he faces each week.
“Romelu hasn’t played from the start for a number of weeks,” he told Birmingham Mail.
“I have a fantastic replacement in Shane Long. Shane has been fantastic for us and didn’t really deserve to be on the bench, but sometimes when you have so many good strikers you have to make decisions.
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“If he’d scored the other two, he’d have put me even more right.
“When you have a squad of players you can’t keep disappointing them all of the time. Romelu has been a good sub for us, and every now and again he’ll get a chance to play.
“Yesterday he got that chance, Shane normally gets the nod and then he’s usually the one coming off – because playing as a lone striker is a difficult shift – but I felt yesterday I wanted to reverse it."
The 49-year-old also suggested that there are positives to be taken from the match, given that his side were perhaps unfortunate to lose.
“Because of the result it’ll be looked at as a negative, but I thought in terms of the performance and the way we played it was a positive,” he added.