The England international striker scored twice to take his tally to 200 goals for United, only the fourth man in the club's history to achieve the feat.
Rooney also set up Antonio Valencia for his side's fourth in a stellar display at Old Trafford as United opened up their UEFA Champions League campaign with a convincing win in Group A.
The 27-year-old, the subject of two rejected bids from Chelsea before the start of the season, could have had a hat-trick if he had converted an earlier first-half chance when he rounded the goalkeeper with the score still at 1-0, but put his shot wide from a tight angle.
Robin van Persie also got his name on the scoresheet for United, with goals from Simon Rolfes and Omer Toprak for Leverkusen the only sour note for Moyes' side.
And the Scot reserved special praise for Rooney's contribution.
Speaking to ITV, Moyes said: "I said about a month ago he's got a real chance to join the greats here at United with his goalscoring record and I thought his goals were great.
"He got round the goalie and that could have been his hat-trick, his second at the time. He was terrific.
"He's been great in training, he's worked hard, he looks fit, he's lean and I think he showed that in his performance again."
Moyes was also happy with the fruitful partnership developing between Rooney and Van Persie, adding: "I think they're both such good players.
"I mean Robin's goal was great, he could have had another as well.
"I said a week or so ago if we can get those two scoring through the season they will be formidable and obviously help get us as many points as we can."
Rooney's future was the focus of great scrutiny after news of Chelsea's interest became public during the transfer window.
But the forward refused to be drawn on whether he asked to leave Old Trafford, and insisted he was just happy to be playing well for the team.
"Listen, I'm concentrating on my football as I said all summer," said Rooney. "I've got my head down and worked hard to get myself fit and ready for the season. I'm delighted with how I've come back.
"I'm delighted to be back playing and scoring. It's a good result, the first game in the Champions League is always important."
