On a disappointing night for the young Rovers, league leaders Newcastle deserved all three points having had the better of the match throughout.
The visitors took the lead on 18 minutes from Gael Bigirimana's fine free-kick, and although Sam Lavelle headed goal saw Rovers level, the Magpies regained their advantage through Callum Roberts soon afterwards.
Hyuga Tanner spurned a great chance to equalise before the break, and that miss would prove costly as the visitors scored their third goal of the night just past the hour mark. Jonathyn Quinn firing home after an error from Kellen Daly.
Chris Brown continued his comeback from injury with another runout for the development squad. The striker came through a hardworking 75 minutes as he continues to build up his fitness. It was one of the bright points on an otherwise disappointing night for Rovers.
Fresh from his appearance as a late substitute for the first team on Saturday against Middlesbrough, Chris Brown was the only senior player on show for Rovers and the striker was the first to threaten on a chilly night at Leigh Sports Village.
Showing a good touch and pace to get past his man, Brown let fly from inside the area but his effort was claimed high by Newcastle goalkeeper Freddie Woodman.
Despite Rovers having the first opportunity in the match, the home side soon found it tough going against lively opposition.
Gael Bigirimana, Olivier Kemen and Alex Gilliead all caught the eye early on and Gilliead and Bigirimana would combine for the opening goal on 18 minutes.
Good forward play from the visitors was brought to a halt as Gilliead was fouled 20-yards out by Kellen Daly.
Gael Bigirimana, one of the more experienced players in the Magpies squad, took the resulting free-kick, hitting a sumptous strike that gave Ryan Crump no chance as it flew into the top corner.
Rovers responded well, Sam Lavelle headed a Connor Mahoney corner kick wide, before from another Mahoney ball Modou Cham wasted an excellent opportunity in front of goal with a weak header that was easily pushed aside.
However from the resulting corner kick Rovers scored. Devarn Green sending the ball into the box to where Daly flicked on and this time Lavelle made no mistake in front of goal to head home the equaliser.
But parity lasted barely four minutes as Newcastle regained the lead just before the half hour. Callum Roberts given the freedom to run at the Rovers back line before planting a low shot into the corner of the net.
Brown and Mahoney both went close as Rovers looked to get back on level terms for a second time. Hyuga Tanner should have done so in added time at the end of the first half, but blazed over from close-range.
Ryan Nyambe replaced Tanner at the start of the second half, with David Carson moving into the centre of midfield to add more bite, but it was the visitors who grabbed the all-important next goal.
Just past the hour mark a poor square ball from Daly was intercepted by Kemen and he quickly found Jonathyn Quinn in space and the forward finished well with just Crump to beat.
Chris Brown and Devarn Green combined well for Rovers' only chance of note in the second half on 71 minutes. The duo playing a one-two before Green curled a shot just wide from the edge of the box.
It would be Brown's last contribution as he was replaced soon after. Jordan Preston on as his replacement after a hardworking 75 minutes. Moments later Luke Wall was introduced with Modou Cham making way.
Both sides worked hard in the closing stages with several crunching - but fair - challenges, with the visitors able to see out the remaining minutes with ease to cement their place at the top of the table.
ROVERS: Crump, Carson, Doyle, Tanner (sub Nyambe 46 mins), Lavelle, Daly, Mahoney, Bauress (c), Brown (sub Preston 75 mins), Green, Cham (sub Wall 79 mins).
Subs not used: Williams, Jones.
Goals: Lavelle 25 mins.
NEWCASTLE: Woodman, Olley, Gibson, Bigirimana, McKinnon (c), Gillesphey, Gilliead, Barlaser, Quinn (sub Broccoli 88 mins), Roberts (sub Longstaff 88 mins), Kemen.
Subs not used: Cameron, Suddick, Ward.
Goals: Bigirimana 18 mins, Roberts 29 mins, Quinn 61 mins.
Booked: Olley 39 mins.