Rovers ended the season in 11th place after losing to the odd goal in five against a Luton Town side who earned Championship survival with the three points.
A good start saw Rovers take the lead inside the opening 10 minutes through a close range Adam Armstrong finish.
However, the Hatters battled back to take a slender advantage into the break through own goals from Hayden Carter and then Bradley Johnson.
A James Colins penalty put Luton firmly in command, but Sam Gallagher's flick set up a big final 15 minutes at Kenilworth Road, but Rovers couldn't force a way through against a resolute Hatters side.
An unchanged Rovers started well in Befordshire, with Johnson's long range effort forcing home goalkeeper Simon Sluga into a fine stop just five minutes into the encounter.
However, it didn't take too much longer for Rovers to deservedly take the lead through Armstrong's close range finish only five minutes later.
A dangerous corner into the box wasn't cleared by Luton, with the ball dropping kindly for the striker to swivel and then swipe home with his left foot for his 16th league goal of a prolific campaign.
Playing with freedom, Lewis Holtby was next to try his luck from the edge of the box, but the German playmaker could only drag wide of Sluga's left-hand post.
Nathan Jones' men finally made a foray forward midway through the half, but Harry Cornick's lofted header looper onto the roof of the net and never troubled ex-Hatter Christian Walton, before Collins nodded wide a moment later.
Despite Rovers' dominance, an unfortunate own goal from Carter levelled things up for Luton just before the half hour mark.
A ball into the box was flicked on, and the young defender inadvertently nodded in via Walton's right-hand post, to hand the home side a lifeline in their battle to avoid relegation.
That lifeline turned into an advantage just eight minutes later when another own goal gave Jones' men the lead.
A dangerous corner was swung in, missed everyone in a Luton shirt, but cannoned off the shin of Johnson and nestled into the back of the net.
A double change at the break saw Lewis Travis and Holtby swapped for John Buckley and Jacob Davenport, and the latter was soon involved in the first notable incident of the second half.
It arrived just before the hour mark when the young midfielder was adjudged to have clipped the heels of Luton attacker Harry Cornick in the box.
Up stepped main marksman Collins, who made no mistake from 12 yards by thumping into the back of the net as Walton dived to his right.
Town's tails were up and only a great header from Darragh Lenihan stopped Collins from getting on the end of Cornick's cross from the right as Luton went in search of wrapping up the points.
Rovers went in search of a route back into the encounter, with Joe Rothwell bending a free kick over Sluga's upright as the clock ticked to just 25 minutes of the season remaining.
Time was running out if Rovers were going to get something from the game, but substitute Gallagher ensured it would be a nervy final 15 minutes for the hosts when he flicked home for his second goal in as many games.
A diagonal ball from Darragh Lenihan was knocked down by Danny Graham, and the striker was in the right place to flick over Sluga and in with the outside of his right boot.
The equaliser almost arrived a minute later, but Buckley's volley was nudged just wide of the post by home skipper Sonny Bradley.
Rovers continued to probe as Jones' side got deeper, with substitute Elliott Bennett firing wide with 84 minutes left on the clock.
Despite throwing everything at Luton, Rovers couldn't find a route past Sluga, with Mowbray's men concluding the season in 11th position.
For the hosts, the win earned survival and a second campaign in the Championship for 2020-21.
Rovers: Walton, Nyambe, Lenihan (c), Carter, Rankin-Costello, Travis (Davenport, 46), Johnson, Rothwell (Bennett, 78), Holtby (Buckley, 46), Armstrong (Gallagher, 61), Brereton (Graham, 61).
Unused substitutes: Eastham, Chapman, Bell, Vale.
Goal: Armstrong, 10, Gallagher, 75.
Booked: Travis, 36.
Luton Town: Sluga, Cranie, Bradley (c), Berry, Lee (Pearson, 78), Cornick (Hylton, 71), Ruddock-Mpanzu, Carter-Vickers, Collins (LuaLua, 71), Bree.
Unused substitutes: Shea, McManaman, Shinnie, Moncur, Butterfield, Kioso.
Goals: Carter OG, 28, Johnson OG, 36, Collins pen 60.
Booked: Cornick, 65, Carter-Vickers, 84, Hylton, 88, Berry, 90+6