The England forward missed from 12 yards last weekend against Arsenal, and scuffed his effort against the Portuguese side into the top corner. Of 26 penalties in all competitions for the Red Devils, the striker has missed nine spot kicks, something which his boss says he needs to improve on.
"I think that Wayne has to accept it," Sir Alex told reporters. "He has to have a better strike rate with penalties.
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"I think he has to accept that he has to produce better. I mean he is capable of hitting them. The one thing about Rooney is it wouldn't matter if it was the World Cup final or a first-round game against an amateur team, he would want to score, there's no doubt.
"And his temperament is that, if he misses, it won't affect him. But that's important for a penalty-kick taker, that it doesn't affect them if he were to miss and that's an issue with a lot of people taking penalty-kicks is if they miss it, how they handle it. Because of Wayne's temperament, it's good that way.
"Oh, no chance [of him not taking another]. No chance. He won't want to miss another one!"
With United having a poor record from the spot this season - a notable miss being Robin van Persie's chipped effort in the 3-2 win over Southampton - Sir Alex has also revealed who he thinks is the best penalty taker in his team.
He added: "I think, probably, the best penalty-kick taker is [Ryan] Giggs. He's never missed one. Well he missed one when he was 17 in the quarter-final tie against Southampton in a penalty-kick shootout but he's never missed one since.
"But he doesn't play every week. I'll have to bring him on like in these American Football games."