Moyes record his first Champions League group stage win as Rooney reached the landmark double nine years after joining the club from Premier League rivals Everton.
Rooney was strongly linked with a move to Chelsea during the close season, but is clearly back to his best as goals from Robin van Persie and Antonio Valencia completed a rousing win for the English champions.
"Wayne was very, very good," said Moyes.
"He has been great in training. He is lean and fit and it showed.
"Wayne played great. He could have got a hat-trick. I said several months ago Wayne Rooney could join the real greats with his goalscoring.
"He's got a real chance to be one of the all-time leading goalscorers at this club, and if he keeps playing as he did [against Leverkusen], he'll get there.
"He looks like he is moving as well as he has done. He is in a good place himself at the moment and obviously any centre-forward who is scoring goals feels good about himself.
"I knew if you are going to win the Champions League you have to have several world-class players and Wayne comes into that category.
"It is really important you have as many of them as you can in your team.
"You can see what some of the other teams have got and we have to keep adding to that while keeping the ones we already have here."
Rooney is the fourth man in United's history to 200 goals or more for United joining fellow legends Sir Bobby Charlton (249), Denis Law (237) and Jack Rowley (211) in passing the mark.
"I am concentrating on my football. I have got my head down and worked hard," said Rooney. "I am delighted with the way I have come back.
"It has gone quickly, my time here. I am really pleased to score 200 goals for a club like Manchester United. It's a great honour."