Moyes has endured a torrid start to life at the helm of the Red Devils, winning just two of his opening six Premier League matches, which include defeats to Manchester City and Liverpool.
"It was always going to change quite dramatically. When someone has been there for over 25 years, whoever was going to take the job was going to have big question marks put against them," Owen told FIFA.com.
"It was going to be a change for everybody within the club. Manchester United have appointed the right man in David Moyes, he has had a good career so far and has done fantastically well at Everton.
"In time he will prove to be a very good choice. They've had a bit of a slow start to the season, but they've had a difficult start to the season. I'm sure they'll get it right though and will still be one of the main challengers at the end of the season."