Goals from Joe Rankin-Costello and Dan Butterworth completed the double over Liverpool, and made it 13 wins from the last 18 games to end their Premier League 2 campaign with the three points at Anfield.
Both of the strikes came in the first half, which Rovers largely dominated on Merseyside, with Butterworth's excellent solo run and finish the pick of the pair after Rankin-Costello's early header.
The Reds did pull a goal back through captain George Johnston late on, but Damien Johnson's charges held on to secure a mid-table finish and complete a brilliant second half of the campaign.
The fine form pulled Rovers clear of the relegation zone a couple of weeks ago, but the team showed their quality and professionalism at Anfield to see the game out and end the term on a high.
Johnson made two changes to his starting XI, with Stefan Mols and Jack Vale returning to the side at Anfield.
The pair came in for Joe Nuttall and Harry Chapman, the latter who came off the bench at Norwich City for the first team on Saturday evening.
Rovers had the better of the early stages without really testing home goalkeeper Caoimhin Kelleher, with Dan Butterworth shooting straight at the Irish custodian just before the 20 minute mark.
But with the next chance came the opening goal as the in form Rankin-Costello continued his scoring streak.
The wing back was upfield and connected with Stefan Mols' excellent cross from the right to nod past Kelleher and into the bottom corner.
Rovers went searching for more, with John Buckley producing a rampaging run from midfield before firing into The Kop after skipping past the challenge of Connor Randall.
At the other end, Rhian Brewster saw a strike blocked by Charley Doyle before Ben Woodburn's curling attempt deflected over Charlie Albinson's upright.
Albinson was in the right place at the right time just a few moments later to stop Rafael Camacho from equalising with seven minutes to go until half time; getting down low to claim the Portuguese winger's effort on goal.
But a minute later and Rovers doubled their tally in emphatic style through Butterworth.
After latching onto Tyler Magloire's long pass, the forward got it under his spell down the left before cutting in and sending a left-footed drive across Kelleher and into the bottom right-hand corner.
That meant Rovers went into the break with the deserved advantage against a Liverpool side who hadn't really troubled the backline too much.
The second half continued in the same vein, with Rovers bossing possession, but it was the Reds who went close to halving the scoreline, but after Adam Lewis' tempting low cross, Randall slashed wide from an acute angle and the opportunity went just after the hour.
Albinson had to be alert to turn over a Camacho curler soon after as the hosts turned up the heat in a bid to find a route back into the encounter, with time running out.
But with six minutes remaining the Merseysiders gave themselves a chance as skipper Johnston capitalised from close range after Rovers failed to deal with Camacho's inswinging corner kick.
It should have made to a nervy ending, but to their credit Rovers saw the game out comfortably, which would have delighted Johnson, who will be proud of his side's season overall.
Liverpool U23s: Kelleher, Whelan, Lewis, Masterson, Johnston (c), Randall, Camacho, Woodburn, Brewster (Gallacher, 72), Christie-Davies, Jones (McAuley, 88).
Unused substitutes: Atherton, Juanma.
Goal: Johnston, 84.
Booked: Camacho, 89.
Rovers U23s: Albinson, Doyle, Thompson, Davenport, Magloire (c), Carter, Rankin-Costello, Buckley, Vale, Butterworth, Mols.
Unused substitutes: Eastham, Annesley, Whitehall, Brennan, Pike.
Goal: Rankin-Costello, 24, Butterworth, 41.
Booked: Butterworth, 52, Buckley, 90.
Referee: Matthew Dicicco.