Goals from Callum Roberts and Joe Kerridge sealed the points for the Magpies as Dave Watson’s side made it seven successive wins.
Aaron Knight scored from the edge of the box for a consolation late on but it could have been a different story had the Whites made their first-half domination pay.
Wanderers had a host of chances to take charge of the match with Jamie Thomas hitting the bar with a fine effort.
But they were punished for wasting those chances as their four-match winning run in the FA U18 Premier League came to an end.
Despite the disappointment, coach David Lee remained typically upbeat after the defeat.
Lee told The Bolton News: “We were by far the better team and, with better finishing, should have scored four in the first half.
“The second half was much the same. We dominated the game and I was pleased with the players’ determination, desire and work rate.
“They did their best to make up for a couple of individual mistakes that cost us two goals against the run of play.
“It was disappointing after a good run of results, but I was pleased with the players’ performances.”
The U18s are back in action on Saturday when they host Manchester City at Lostock, kick off 11am.