A first half strike from Lewis Mansell set Damien Johnson's side on their way, and they looked set for all three points after Newcastle defender Callum Williams could only head a Willem Tomlinson centre into his own net.
However the Magpies ensured a nervy finish at Leigh Sports Village when substitute Callum Roberts made it 2-1 with 12 minutes remaining.
The visitors had chances to equalise in the closing stages, but the young Rovers held on to claim all three points.
Rovers went into the match looking to make it five wins from their last seven league outings and after an even start at Leigh it was they who grabbed the opening goal of the game on 18 minutes.
Good pressure from the blue and whites saw a backpass seized upon by Lewis Mansell and he made no mistake for his fourth goal for the Under-21s this season.
It was almost 2-0 three minutes later as Connor Mahoney picked out David Carson on the edge of the box, but Freddie Woodman in the Newcastle goal got down well to save.
That prompted the Magpies into action, the experienced Sylvain Marveaux was just wide with a 20-yard free kick.
Then following a spell of Newcastle pressure, forward Lewis McNall got a shot away but it was comfortable for David Raya, before a corner found it's way to Lubomir Satka, but the defender shot wide at the back post to ensure Rovers would lead at the break.
Like the first, the second half was slow to get going, Marveaux denied by the linesman flag after outpacing the Rovers' defence.
Whilst at the other end Carson fired over the angle, before Mansell couldn't make the most of a Scott Wharton header from a corner as he glanced wide.
On 72 Rovers finally doubled their advantage courtesy of an own goal. Good work down the right by Ryan Nyambe saw the defender feed Willem Tomlinson and as his ball was lofted into the area in search of Sam Joel, half-time substitute Callum Williams could only nod it over Woodman and into the back of his own net.
Rovers looked to ram home their advantage as Devarn Green and Connor Mahoney went close, but instead it was the Magpies who grabbed themselves a lifeline with 12 minutes to go.
After their pressure resulted in a corner kick on the right, the ball was sent to the far post to where sub Callum Roberts slammed home.
Having been pegged back from a two-goal lead just seven days ago at Aston Villa, Rovers had to defend resolutely to prevent it happening once more. David Raya with a brilliant one-handed save to deny Jamie Sterry in the closing stages to ensure the development squad ended 2015 on a high.
ROVERS: Raya, Nyambe, Askew, Tomlinson, C. Doyle, Wharton (c), Mahoney, Carson, Mansell, Joel (sub Rankin-Costello 85 mins), Green.
Subs not used: Rittenberg, Crump, Makinson, Howarth.
Goals: Mansell 18 mins, Own goal 72 mins
NEWCASTLE: Woodman, Sterry, Laidler, Hunter, Mbabu (sub Williams 46 mins), Satka (c), Gallacher, Barlaser, McNall (sub Roberts 53 mins), Marveaux (sub Longstaff 75 mins), Smith.
Subs not used: Pearson, Gibson.
Goals: Roberts 78 mins