The Bosnia international had been on the pitch for just over a minute when he pounced on John Arne Riise's poor header to seal a win for the champions.
City take on Borussia Dortmund in the Champions league on Wednesday and Mancini is keen to keep his attackers fresh for their upcoming clashes.
He told Sky Sports News: "It’s difficult for me to make the decision every time, but we have another game in three days. An important game. Today we played with all strikers but they should accept this. In a top team it’s like this.
"It’s difficult because I know that I have good players and when I choose 11 players the other seven go on the bench. For this reason it’s very difficult and also for the players."
|19/1||Manchester City are 19/1 to beat Borussia Dortmund 3-2 with Paddy Power|
"We played a very good game," Mancini continued. "Very good football and we scored two goals but we could have scored another two or three goals.
"It was difficult because it wasn’t a penalty. After that with 20 minutes gone you’re 1-0 down with a penalty that wasn’t a penalty, it’s difficult but I think the guys played very well. We continued to play football, we stayed calm.
"There are some moments where even if you have good players you can’t score. Today was another game like this. We had a lot of chances and we scored in the last three minutes."
City have endured stuttering form in the early throes of the season, but Mancini preferred to draw positives from the result, and believes his side will be contenders by the end of the season.
He concluded: "It’s very important to stay with Chelsea or United in a difficult moment like we have but the season will be long and I think we’ll have a big chance."