Rovers were hit by a last-gasp winner as Chris Eagles stole all three points for Bolton Wanderers at the Reebok.
The Trotters substitute scored the only goal of the game with almost the last kick of the match as Rovers suffered a 1-0 defeat.
There was little to choose between the two sides throughout, Grant Hanley going closest in the first half with a shot that clipped the crossbar, the Scot would hit the bar five minutes into the second half also as Lonergan tipped the ball over.
Bolton weren't short of chances either, David Ngog fired over when well placed before Jake Kean saved from Medo Kamara and Adam Henley cleared off the line to deny Lee on the follow-up.
As the match entered the final stages Jordan Rhodes was thwarted by Lonergan, then David Jones was narrowly off target with a delicate lob.
The match seemed destined to be a hardfought draw until Eagles stole in to fire in off the far post at the death.
After last Saturday's loss to Peterborough Michael Appleton made four changes to his starting eleven for the match against Bolton.
After impressing as second half substitutes at the weekend, Cameron Stewart and David Jones were both given their first starts whilst Adam Henley and Morten Gamst Pedersen were also back in the eleven.
Making way were Bradley Orr, Danny Murphy, Karim Rekik and David Bentley, whilst there was a place in the 18-man squad for Leon Best for the first time this season.
A rousing atmosphere at the Reebok saw the two sides go at each other from the off. Inside the first minute Darren Pratley volleyed narrowly over the bar for the hosts, whilst Scott Dann found space at the back of the Bolton box but couldn't direct the ball goalwards.
A quick break from a Rovers corner saw the home side threaten once more, Pratley showing good pace down the left to find David Ngog with a ball into the area but the Frenchman could only divert it wide.
A good turn in the area from Jordan Rhodes saw Cameron Stewart drill the ball wide of goal before a cross-turned shot from Pratley required quick reactions from Jake Kean at the near post. Then only a great last-ditch tackle from Jason Lowe denied Ngog a goalscoring chance.
The closest either side came to opening the scoring in the first half came on 40 minutes. After Cameron Stewart had been fouled on the left touchline, Morten Gamst Pedersen delivered the resulting free-kick into the box, it was hit low as Grant Hanley stuck out a boot to divert it goalwards only to see it clip the crossbar and bounce behind.
The first half ended with Grant Hanley heading onto the woodwork and the second half would start in a similar manner.
On 51 minutes a Markus Olsson centre picked out the giant Scot but his looping header was touched onto the woodwork by Andy Lonergan.
Like the first half, both sides showed plenty of endeavour, looking to get the ball forward at every opportunity.
On 64 minutes Marcos Alonso tested Rovers from a 25 yard free-kick. The ball got passed the wall but not Jake Kean who dived to his right to make the save.
Then David Ngog somehow blazed over as a long throw reached him in the six-yard box.
After more than seven months on the sidelines Leon Best made his long-awaited debut in a Rovers shirt, the striker replacing DJ Campbell with ten minutes remaining.
Within seconds he almost unwittingly claimed an assist as he pressured Marcos Alonso into playing the ball back towards his goal, Jordan Rhodes stole in to shoot but Andy Lonergan made a sharp save.
That chance sparked a host of opportunities for both sides as the game entered the final stages, on 85 minutes Medo Kamara saw a shot pushed out by Kean, Lee stole in to shoot goalwards but Adam Henley was there to clear off the line.
The resulting corner prompted an almighty scramble, Kean showing great awareness to block as Craig Dawson closed in.
Then it was back up the other end as Cameron Stewart sent a ball over to the back post, Rhodes rose at the back post but Lonergan again tipped over the bar.
Deep into the three minutes of added time came the final two chances and unfortunately for Rovers the last one would be taken.
David Jones's delicate lobbed deserved to win the game bit the ball flew an inch over the bar.
From the goal kick the ball was hit forward quickly to where Chris Eagles advanced along the edge of the area before hitting a low shot back across Kean that crept in off the far post.
It was desperately unlucky for Rovers as they had worked tirelessly and created a host of chances against the Wanderers only to lose it at the death.
Rovers have a quick turnaround, the small matter of the FA Cup quarter-final against Millwall this Sunday at the Den.
BOLTON: Lonergan, Ricketts, Dawson, Knight, Alonso, Spearing, Pratley (sub Eagles 71 mins), Lee, Ngog, Kamara, K. Davies (c) (sub C. Davies 76 mins).
Subs not used: Lynch (GK), Wheater, Holden, Sordell, Odelusi.
Goals: Eagles 90+3 mins.
ROVERS: Kean, Henley, Dann (c), Hanley, Markus Olsson, Pedersen, Lowe, Jones, Stewart, Campbell (sub Best 80 mins), Rhodes.
Subs not used: Sandomierski, Orr, Givet, Nuno Gomes, Rekik, Bentley.
Booked: Lowe, Hanley.