Just 15, the striker was a second-half substitute as Darren Fletcher's U18 team won 1-0 on Merseyside.
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United captain Amir Ibragimov's first-half penalty was enough to separate the two teams on the day.
Australia youth international fullback James Overy started for United, along with 14 year-old winger JJ Gabriel, the son of former Republic of Ireland international Joe O’Cearuill.
Rooney, the son of former United and England captain Wayne Rooney, was a 73rd minute substitute and lifted the visitors' energy in attack in the final 20 minutes.