The first leg was played on Monday evening and skipper Sam Hewson put Manchester United's youngsters on target for their 10th FA Youth Cup triumph with a late penalty at Anfield.
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Holders Liverpool had taken the lead in the first half with a fine header from the impressive Craig Lindfield.
But in front of a 19,518 crowd, an own goal from Robbie Threlfall gave United parity soon after the break, before Hewson bagged his fifth goal in this season's tournament to send United confidently into the Old Trafford second leg on April 26.