Bolton's hoodoo over Rovers shows no sign of abating after the visitors suffered their sixth successive defeat at the Macron Stadium.
A moment of carelessness at the back 12 minutes from time saw Gary Madine score the only goal of the game to earn the Trotters just their second win of the season.
Rovers started brightly in the lunchtime encounter but it was Bolton who should have opened the scoring, Zach Clough seeing his poked effort rebound off the upright.
Paul Lambert's side saw plenty of the ball after that but created only half-chances, Ben Marshall and Danny Guthrie off target from distance.
The second half followed a similar pattern with little in the way of quality play, Shane Duffy twice heading over, Danny Guthrie firing straight at Ben Amos.
But just as it looked as if the game would end goalless like the reverse fixture back in August, the home side struck. Moxey's long throw wasn't picked up and Madine had time to control the ball on his chest before turning and firing home.
That prompted Rovers into action in the closing stages, but the closest they would come to getting back on level terms would be in added time when substitute Tom Lawrence saw his shot strike the post, but the ball rebounded into the grateful arms of Amos.
With Corry Evans failing to make the squad due to a groin strain, Paul Lambert kept faith with the same starting XI that suffered a first defeat under his charge last time out at Reading.
And that familiarity saw Rovers start the game on the front foot, Fode Koita holding the ball up well for Ben Marshall, but the wide-man's shot was well off target.
But despite hardly having a kick in the opening exchanges, the home side should have taken an eighth minute lead.
The returning Mark Davies, one of four changes to Neil Lennon's side following their Boxing Day drubbing at the hands of Rotherham United, made progress down the left to feed Dean Moxey, his centre was met first time by Zach Clough six yards out but the striker's effort slammed off the post.
The rebound fell for the recalled Gary Madine, but the ball wouldn't drop quickly enough and Markus Olsson was able to clear the danger.
That chance settled early jitters from the Trotters, with Rovers now being the side who were sloppy in possession.
But despite very little quality on show it was Rovers posing more of a threat in the attacking third. Marshall was wayward from distance, before his dangerous ball to the back post had to be put behind by Moxey with Koita lurking.
The resulting corner saw a scramble cleared as far as Danny Guthrie, but the Rover, who once enjoyed a loan spell with Bolton, blazed high over the bar.
Three minutes before the break play opened up as Craig Conway claimed possession, but he took too long to feed Jordan Rhodes and the striker's eventual effort was blocked. It summed up a poor first half showing.
Rovers were then forced into a change just before the half-time whistle was blown as Koita limped off with what looked like a hamstring strain. He was replaced by Nathan Delfouneso for his first taste of action under Lambert.
There was more of a derby feel to the start of the second half with a few crunching tackles and a flurry of bookings.
Following a rash challenge on Conway for which Moxey saw yellow, the Scot sent the resulting free-kick into the area, but whilst Shane Duffy got a decent connection on the cross he wasn't able to guide his header on target.
Then a strong forward run from Delfouneso lead to a spell of Rovers pressure, but Akpan could only fire wide after the ball reached him on the edge of the box.
At the other end good defensive work from Grant Hanley saw the Rovers captain force Zach Clough to poke wide, before a cross from the right picked out Madine but having mis-timed his jump the header went well wide.
In what was becoming an increasingly stretched encounter Rovers responded with further chances themselves. Guthrie firing straight at Amos, before Duffy again was off target with a header from a corner.
Rovers replaced Jordan Rhodes with Tom Lawrence, but within sixty seconds they found themselves a goal down.
A Moxey throw from the left found it's way to Madine and he held off Duffy, he controlled the ball on his chest before turning and firing beyond Steele.
Needing a response and quick Henley made progress down the right, but as Conway sent the ball into the area, Lawrence's flick cleared the bar.
And with time running out Rovers threw bodies forward in search of an equaliser, leaving them exposed on the break. Bolton seeing claims for a penalty waved away after Josh Vela shot looked to strike a Rovers arm in the box.
In added time Rovers were the width of a post away from levelling as Lawrence prodded goalwards, the ball took a deflection to beat Ben Amos but it rebounded off the far post and into the grateful arms of the Bolton keeper.
The result means a sixth straight loss for Rovers at Bolton, the Wanderers must wish they could play their near-neighbours every week.
BOLTON: Amos, Prince, Moxey, Vela, Feeney, Clough, Madine, Davies, Pratley (c), Wheater, Holding.
Subs not used: Rachubka (GK), Spearing, Danns, Casado, Wellington, Dobbie, Wilson.
Goals: Madine 78 mins.
Booked: Davies, Moxey, Vela, Pratley.
ROVERS: Steele, Henley (sub Taylor 88 mins), Duffy, Hanley (c), Olsson, Conway, Guthrie, Akpan, Marshall, Koita (sub Delfouneso 45 mins), Rhodes (sub Lawrence 77 mins).
Subs not used: Eastwood (GK), Spurr, Kilgallon, Williamson.
Booked: Akpan. Duffy
Attendance: 18,048 (including 3,784 Rovers fans).