Grant Hanley played just over an hour on his return to action as a young Under-21s ended their season with a narrow loss at home to Bolton.
The Rovers captain showed no after effects of his calf injury as he came through 63 minutes at a sunny Brockhall.
Rovers were the better side throughout but without reward, however the game was decided three minutes from time when Bolton were awarded a penalty after Hyuga Tanner fouled Connor Wilkinson inside the box.
Wanderers sub Jamie Thomas stepped up and clinched victory for the visitors from 12-yards.
In charge of the Under-21s for the last time, coach Eric Kinder made ten changes from the side that lost less than 48 hours earlier against Newcastle United.
Naming the youngest development sides of the season, the starting XI saw debuts for Academy 1st year scholars Andrew Fisher, Lewis Travis, Scott Wharton and Willem Tomlinson.
Wharton would have the first chance of the game on 11 minutes when the defender connected well with a Lewis Hardcastle free-kick, but Harry Campnell in the Bolton goal claimed high.
Lewis Mansell worked tirelessly up front, on 20 he fired narrowly wide after beating his man to the ball, before hooking a shot over on the turn soon afterwards.
Marshalled superbly by Grant Hanley, the visitors offering little as an attacking force. With play very much centred around the Bolton box.
The Wanderers were indebted to a goal-line block from captain Quade Taylor to stop a shot from Hyuga Tanner to ensure it was goalless at the break.
Rovers continued to force the pace into the second half, a flowing move saw Hardcastle and Mansell combine to feed Modou Cham, but the winger saw his shot saved by Campbell.
It wasn't until the hour mark that Andy Fisher in the Rovers goal was called upon to make a save. The keeper getting down well to keep out an effort from Connor Wilkinson.
Hanley made way soon afterwards with Sam Lavelle on in his place, defensive partner Wharton nodded wide a Hardcastle set-play as Rovers looked to break the deadlock.
It almost came on 79 minutes when an outstanding run from full back Lewis Travis saw the defender race through on goal, but his low shot was well saved.
With the match increasingly looking like it would end goalless, it was an error from Tanner that decided it. The Australian taking a touch too many in his own area and in doing so brought Bolton forward Wilkinson down for a penalty kick.
Substitute Jamie Thomas stepped up and although Fisher dived the right way the Bolton man squeezed the ball home.
Rovers subs Connor Mahoney and Sam Lavelle combined in the closing stages as the home side went in search of a deserved leveller, but defender Lavelle headed over when well placed.
ROVERS: Fisher, Travis, Edgar, Hardcastle (c), Hanley (sub Lavelle 63 mins), Wharton, Cham (sub Mahoney 74 mins), Tomlinson, Mansell, Tanner (sub Thomson 88 mins), Wall.
Subs not used: Rittenberg, Crump (GK).
BOLTON: Campbell, Maher, Holding, Taylor (c), Boben, Perry, Iliev (sub Newby 76 mins), Lussey, Woolery, Wilkinson, Odelusi (sub Thomas 72 mins).
Subs not used: Fitzsimons, Spooner, Cvetko
Goals: Thomas 87 mins