The Germany striker didn't get onto the pitch until the final half-hour as Barca won 2-1 on Thursday night.
Howe said: "I can't live in that world, I have to make decisions for the benefit of the player sometimes.
"It was a really difficult one for Nick, of course any player would want to start every game but I have to try to manage him into the team.
"And make sure he stays fit and that was always at the heart of this decision. Knowing that we have Anthony suspended for the next game as well.
"It is the same for Jacob Murphy as well, he is nursing an achilles problem and we just want to keep the majority of the squad as fit and healthy for as long as possible."
Marcus Rashford's double defeated Newcastle, with Anthony Gordon's late goal coming too late.
Howe said: "We were really in the game. I never felt we were out of it. I'm disappointed we didn't score the first goal.
"That was crucial. We had the chances to do it. It was a whole-hearted gutsy display but maybe lacking the quality to get us the win.
We wanted to create a difficult environment with high-octane football. I think it was there. We didn't get the bounce of the ball off the presses.
"The chances were there in the first half. Against teams like this you won't get many. We got punished."