Dan Pike's early strike wasn't enough for Rovers to end their Group G campaign on a high in an even clash against local rivals Burnley at Curzon Ashton's Tameside Stadium.
As it was, the result didn't matter for either side, with Rovers finishing top of Group G whatever happened, and Burnley guaranteed to finish third.
For Rovers, they will host Wolves in the last 16 of the competition, with a date to be confirmed in due course.
There was a large chunk of fortune with Pike's sixth minute opener, which was caught in the wind before deceiving Lucas Jensen and looping into the back of the net.
But Burnley battled back, and Joel Mumbongo's well struck strike was probably deserved on the balance of play in tough conditions in Greater Manchester.
A youthful side was named by Billy Barr, with a number of the team who earned a place in the semi-finals of the FA Youth Cup after defeating Arsenal last week earning a starting berth.
Luke Brennan and D'Margio Wright-Phillips were rewarded for their goalscoring exploits against the Gunners by beginning on the wings, with two-goal hero Sam Burns also starting up front.
At the back, Tyler Magloire and Louie Annesley were part of a back four that also featured Enzo Boyomo and Pike, who was filling in at left back following Lewis Thompson's recent move to AFC Fylde.
A fast start from Rovers saw Barr's side take the lead after only six minutes, with Pike's cross-shot being caught in the wind and wrong-footed Jensen, who got a touch on the attempt but couldn't keep it out.
The Clarets went in search of an immediate equaliser, but Ne-Jai Tucker's free kick comfortably sailed just over Joe Hilton's upright.
The next chance came the way of Burnley again, with Hilton out quickly to deny Chris Conn-Clarke with his feet from close range.
Rovers controlled the game, but didn't really come close to adding to their tally until a minute before the interval.
This time it was Stefan Mols' driving run towards the edge of the box that opened up the space, but the midfielder saw his strike clatter against the left-hand post before bouncing behind.
That meant Rovers went in with a slender advantage against their near neighbours, but would have counted themselves unfortunate to have not added more daylight to the scoreline at the break.
A half time alteration saw Jalil Saadi enter the action in place of Boyomo, with Magloire shifting across from right back to centre back.
It was a Burnley substitute that ensured the Clarets found an equaliser just after the hour mark.
Mumbongo had only been on the pitch for nine minutes, but that was all it took for the striker to latch onto a through ball and drive a low attempt past Hilton and into the bottom left-hand corner to level for the hosts.
The encounter became scrappy in the late stages, with neither side really doing enough to earn the win, and the draw was probably the fairest outcome in an even contest.
Burnley Under-23s: Jensen, Patterson, Koiki, Brennan, Thomas (c), Pruti, Tucker, Woods, McGlynn, Thomson (Mumbongo, 55), Conn-Clarke.
Unused substitutes: Allan, Senior, Rooney, Moonan.
Goal: Mumbongo, 64
Booked: McGlynn, 73, Brennan, 90, Woods, 90.
Rovers Under-23s: Hilton, Magloire (c), Pike, Paton, Boyomo (Saadi, 46), Annesley, Wright-Phillips (Gilsenan, 70), Harlock, Burns (Durrant, 85), Mols, Brennan.
Unused substitutes: Dowling, Wyatt.
Goal: Pike, 6
Booked: Wright-Phillips, 31, Burns, 74, Magloire, 84, Mols, 90.