In a keenly-fought contest between two hardworking sides, it was the Lancashire club who claimed the win with two late goals.
Trialist Maic Sema came the closest to breaking the deadlock in the first half with a header that struck the bar, whilst at the other end a shot on the turn from Lois Maynard was well kept out by Rovers keeper David Raya.
The young Rovers had to defend stoutly at the start of the second half, but their endeavours were rewarded as they scored two goals in the closing stages.
Trialist Jeffrey Sarpong opened the scoring with 14 minutes remaining with a shot from outside the box, before substitute Connor Mahoney ensured a successful night on Merseyside.
With a match against Oldham Athletic on Saturday and a few senior players nursing knocks, Rovers named a youthful squad to face the Vanarama National League side.
New signing Sacha Petshi was joined in the starting XI by trialists Liam Nolan, Jeffrey Sarpong and Maic Sema, with the rest of the side gleaned from the Under-21 squad.
It was Swede Sema who would have the first chance of the game after just five minutes. As the travelling fans urged Petshi to shoot from distance, he instead spread play wide to David Carson. The advancing full-back put a teasing centre into the box which was met well by the head of Sema but whilst his effort beat keeper Scott Davies, the ball glanced away off the crossbar.
Sema and fellow forward Anton Forrester caught the eye in the opening exchanges. The pair linking up well down the flank but striker Forrester was just unable to get the return pass under control in the area.
Tranmere full-back Liam Hogan had the home side's first effort of note just before the quarter-hour, but his 25-yard strike was high into the visiting fans behind the goal.
Midfielder Steven Jennings would go closer, but his first-time shot deflected wide off young defender Scott Wharton.
On a zippy surface there was a good tempo to the game between the two hard-working sides, but chances were at a premium.
A shot on the turn by Lois Maynard that was pushed aside by David Raya was the closest Tranmere came to opening the scoring, whilst an effort late in the half from Jeffrey Sarpong was comfortably saved by Davies to ensure the scores were level at the break.
Rovers made at the resumption of play with Jordan Preston, who spent the second half of last season on loan at Ayr United, replacing Anton Forrester up front.
Almost immediately the Scottish Under-19 international was in the thick of the action. After excellent work on the left by Sema he picked out the forward with his centre but Preston could only fire over the bar from close-range.
The home side hit back with opportunities of their own. Maynard forcing Raya into a low save at his near post. Then a chance on the break followed but the midfielder snatched at the opportunity and fired high over the goal.
In what was proving to be an excellent test for the young Rovers, the majority of which had featured in the final 15 minutes of the match against Rochdale on Tuesday. Tranmere pressed again, with one of their many trialists flashing an effort just past the post on 62 minutes.
New signing Sacha Petshi
Rovers responded with their best opportunity of the second half as our trialists combined. Sema sending a delightful ball across the area but Sarpong could only direct his effort wide of target at the back post.
Just as both sides looked to ready a host of substitutions it was the Lancashire Rovers who broke the deadlock on 76 minutes.
Working the ball well to the edge of the area, trialist Sarpong atoned for his earlier miss by firing home from 20-yards, the ball possibly taking a deflection en route to goal to wrong-foot Davies.
Jeffrey Sarpong scores
That proved to be Sarpong's last involvement as he and Sema were replaced by Connor Mahoney and Luke Wall a minute later and Mahoney would soon make his mark.
There was some lovely one-touch football on view as Rovers attacked down the left with nine minutes remaining, Mahoney taking up possession to play a one-two before advancing to fire home from inside the area.
Bowyer's young guns could have had more goals in the closing stages as Connor Thomson and David Carson both went close, but they'll have been delighted with their night's work on Merseyside.
TRANMERE: Davies, Hogan, Sutton, Ihiekwe, Hill, Maynard, Harris, Jennings (c), Ridehalgh, Stockton, Mangan.
Subs: Pilling, Duggan, Gumbs, Fleming, Clarke, Cringle, Jago.
ROVERS: Raya, Carson, Doyle, Nolan, Lavelle (c), Wharton, Sarpong, Petshi, Forrester (sub Preston 46 mins), Thomson, Sema (sub Mahoney 77 mins).
Subs not used: Mansell, Fisher, Wall.
Goals: Sarpong 76 mins, Mahoney 81 mins.