Villa's youngsters were edged out in a seven-goal thriller on Tyneside in this Barclays U18 Premier League clash.
Jerell Sellars scored twice from the spot, while Callum Robinson was also on target for Tony McAndrew's team.
But it wasn't enough to earn a share of the spoils as the home side collected a maximum haul.
Andy Hall beat Villa keeper Brad Watkins with a neat finish to give Newcastle an early lead.
On 13 minutes, Sellars equalised with a penalty after a mistimed challenge from Macaulay Gillesphey.
The visitors had a great chance to take the lead although Newcastle keeper Freddie Woodman made a fine save to deny Daniel O'Brien.
It allowed Newcastle to capitalise and just after the hour mark Adam Armstrong found the top corner with an unstoppable shot.
Moments later, Hall tapped in his second of the game to make it 3-1.
Villa, though, found a way back into the match with Sellars winning and then converting another penalty.
Armstrong capitalised on a mistake at the back to make it 4-2 before Robinson scored a near post header late on to reduce the arrears again.
But Newcastle held on to secure the victory.
VILLA: Watkins, Lyden, Wildin, Cowans, Webb, Kinsella, O'Brien, Calder, Sellars, Crooks, Abdo. Subs: Dempsey [for Calder, 81], Forth, Zazrivec [for Crooks, 70], Robinson [for O'Brien, 58].