Rovers Under-18s suffered a first defeat in just over two months as Wolves inflicted a maiden loss on Billy Barr's side following an unbeaten fiv-game run in all competitions.
The narrow win moved Wolves level on points with Rovers, who dropped to eighth place in the Under-18 Premier League North table.
Rovers didn't start well at the Sir Jack Hayward Training Ground, and it was the hosts who took the lead early on as Chem Campbell profited after the visitors failed to clear their lines properly.
And that was how the score remained for a large chunk of the game as both sides cancelled each other out.
However, with time running out, a loose ball at the back post fell kindly for Jalil Saadi, who prodded home from close range with just 10 minutes of the clash left.
But just when it looked as if it would end all square, substitute Conor Carty made the impact to play his part in the winner for Wolves.
It was his run and cross down the left side that found Austin Samuels in the box, and the striker slammed the ball home past Ben Winterbottom to seal the points for the home side.
Rovers are next in action on Wednesday 5th December in the FA Youth Cup against Gillingham at Ewood Park, kick-of 7pm.
Wolves: Smith, Richards, Taylor, Trialist, Berkoe, Campbell, Perry, Thompson, Corbeanu (Cundle, 68), Samuels, Forrester (Carty, 75)
Rovers: Winterbottom, Whitehall, Pike, Zimba (Connolly, 81), Barnes, Boyomo, Brennan (Connell, 68), Piliukaltis, Vale (Burns, 68), Wilson, Saadi