Despite recent controversies Rooney showed no signs of mental anguish against Otelul Galati, expertly converting two penalties to take his competition goal tally to 26 - two more than previous record holder Paul Scholes.
It was a vital first win for United in the Champions League this season, but it wasn't all easy going in Romania with Nemanja Vidic receiving a straight red card for a studs-up challenge after 67 minutes.
By this stage Rooney had already opened the scoring but Otelul, playing in the competition for the first time, created several goalscoring opportunities and almost equalised shortly after Vidic's dismissal.
United regrouped with Jonny Evans brought on to shore up the defence, and Rooney's second penalty just before full time secured the victory.
Sir Alex Feguson felt the result was deserved, but paid credit to Otelul ahead of the two clubs' re-match at Old Trafford on November 2nd.
"I don't think we were lucky. We were the better team," said Ferguson.
"We dominated possession and improved in the second half, particularly through Nani, Anderson and Rooney. Those three players changed the game."
"They (Otelul) are a very hard-working and organised team. Their coach should be pleased. It's not easy to chase the ball all night and they should take credit for that."
In contrast to Ferguson's comments, Manchester City manager Roberto Mancini felt his side were fortunate to claim their first Champions League victory courtesy of a last-minute winner from Sergio Aguero at the Etihad Stadium.
Mancini said: "We were lucky because you need luck to score in the last seconds but we deserved to win."
Indeed City were much improved from their last outing in Europe against Bayern Munich, and on this occasion an Argentine was willing to come off the bench to seal a win for his manager.
Having drawn and lost their first two matches in Group A, City required three points against Villarreal to keep alive their hopes of reaching the knockout stage. The task was made more difficult when Villarreal, with only one win in their previous nine games, scored after just four minutes.
With City struggling to create chances Mancini opted to make a tactical substitution before half time, replacing Adam Johnson with Gareth Barry. And the Italian can claim that his decision was instantly vindicated; the equaliser coming three minutes after the change when Carlos Marchena turned Aleksander Kolarov's cross into his own net.
The goal served as a timely confidence boost and the hosts were much more impressive in the second half until they were rewarded by Aguero's late goal.
Mancini was delighted with City's first win, but stressed the challenge his team face when they travel to Spain for the return match in two week's time.
"I hope Sergio's goal will prove to be very important for us. It was really important to win our first game in the Champions League," said Mancini.
"At this moment everything can happen in the group but we also know when we go to Villarreal in 15 days it will be a hard game because they are a very good team who played really well."