The Toffees have made an excellent start to life under Roberto Martinez and Howard does not expect the 3-1 loss at the Etihad Stadium to have any long-term negative effects.
Romelu Lukaku gave Everton the lead but City hit back a minute later through Alvaro Negredo and were well worth the three points.
Howard said: "It wasn't a good day for us but it's been good. We're going into the international break and hopefully when we finish the break we'll start another run.
"We're going to be disappointed of course but it's a tough game away from home. City are one of the best in the country if not the best.
"We didn't play particularly well and I think that's actually a positive. If we'd have come here and given everything and played brilliantly and got a pasting, that would be tough.
"But that's why we're disappointed, because we didn't play particularly well, certainly not how we've been playing the last six or eight weeks. We'll take that away from the game and get better."
City moved in front just before the break through Sergio Aguero, and the timing of the goal was a major blow for the visitors.
Howard said: "It was crucial for them but we're still in the game at 2-1 and the second half is always going to be a chess match in terms of how much to throw forward and at what time.
"It's when it goes to 3-1 or 2-2 that there's a turning point. Once they got the third goal it killed it off. That was always the danger because we had to commit numbers forward."