Speculation that Rooney would leave Old Trafford gripped the club for a number of days before the new contract was signed.
But when asked what affect the uncertainty had on the club, Owen said: "I don't think any, really.
"Everyone seems to be happy now. The club have got a world-class player signed for five years and obviously Wayne's happy and the manager's happy.
"Wayne is obviously ambitious and the club's ambitious. He wouldn't have signed if he had any doubts.
"I don't think there was a change of mind. The press can look into things like that, the why and what and all the rest of it."
United boss Sir Alex Ferguson revealed both he and the rest of the squad received an apology from Rooney for his comments regarding the club's direction, and Owen feels the 25-year-old was right to do so.
He said: "If there was any confusion, then maybe so.
"A lot has been made out of it but half of it is just to fill papers because of the size of the club and the stature of the player.
"Cutting out all the rubbish, the main thing is that he's signed.
"It's better having Wayne Rooney in your squad than not, so we're all happy in that way."