Rovers suffered their first league defeat of 2014 as two goals in each half gave Nottingham Forest all three points.
A whirlwind start from the home side saw them create a host of chances, eventually scoring twice from the penalty spot.
The first coming on 15 minutes after Grant Hanley was adjudged to have fouled Henri Lansbury, the second on 34 after a clumsy Adam Henley challenge. Both penalties were converted by Lansbury. The Rovers bench far from impressed with the officiating.
The home side could have had more in a first half they bossed, but there was a glimmer of hope as Ben Marshall pulled a goal back eight minutes from the break. Curling home his second goal in Rovers colours from 25 yards.
The second half saw Rovers press for a leveller, Tommy Spurr twice going close. Then substitute Josh King was denied by a Karl Darlow save.
With Rovers pressing they were caught on the counter, Jamie Paterson creating and finishing the chance to put the game beyond the visitors.
The visitors ended the match with ten men after Scott Dann limped off and although they continued to look for a way back into the game, they were caught once more, Andy Reid scoring with almost the last kick of the game.
Three changes were made from the side that were knocked out of the FA Cup by Manchester City in midweek.
With Paul Robinson missing out with a hamstring injury, Simon Eastwood returned in goal, whilst Scott Dann was back to captain the side with Matt Kilgallon dropping to the bench. Rudy Gestede returned up front in place of DJ Campbell.
After missing training all week Jordan Rhodes could only get a place on a substitute's bench that featured David Goodwillie following his loan spell with Dundee United.
For the home side, they made four changes from their draw at Bolton Wanderers last time out. A place on the bench for former Rover Matt Derbyshire.
Whilst it was Rovers with the first opportunity at goal, it was the home side who had the better of the opening exchanges.
Just three minutes in and Rudy Gestede showed excellent battling qualities to get the better of Greg Halford and then Gonzalo Jara before poking it past Halford once more but his shot across the area flashed wide.
The home side responded with a flurry of chances that would ultimately lead to the opening goal.
A swirling shot from Jamie Paterson was well dealt with by Eastwood before a Greg Halford header from an Andy Reid free-kick was just off target.
Simon Cox was the next to miss as he somehow put the ball wide from Paterson's cutback, then only an outstanding save from Simon Eastwood prevented Henri Lansbury giving the home side the lead. Shooting from distance, the former Arsenal youngster's shot seemed heading for the bottom corner until the Rovers' 'keeper dived to touch it around the post.
However the pressure continued but the was a touch of generosity about the penalty decision awarded to Forest on 14 minutes.
With Grant Hanley and Henri Lansbury chasing the ball towards the corner, Lansbury got in front of the Scotsman only to be bundled over in the box. The referee pointed to the spot.
Lansbury took the honours from 12 yards and just about converted, Eastwood dived the right way but the ball squirmed underneath the Rovers and into the corner of the net.
Rovers had rare incursions into the Forest box, Rudy Gestede got up well to meet a Tom Cairney free kick but could only head over, then from a Ben Marshall free-kick Scott Dann headed back across the area but the home side cleared their lines.
A jinking run from Tom Cairney was halted by Dan Harding and from the resulting 20 yard free-kick the midfielder was a whisker over, his left-footed curler just going the wrong side of the crossbar.
But just as Rovers appeared to be building up a head of steam another penalty decision went the way of the home side. Adam Henley slid clumsily into Jamie Mackie and the official had no hesitation in pointing to the spot once more.
Lansbury stepped up once more and drove high into the roof of the net giving Eastwood no chance.
"2-0 to the referee" chanted the visiting fans, but needless challenges in dangerous positions had proved extremely costly.
Three minutes later and Rovers pulled an important goal back. After a corner had been cleared to the far side, it back back to Tom Cairney who shaped to shoot only to switch it to Ben Marshall 25 yards out and the former Leicester man unleashed an unstoppable shot beyond Darlow in the Forest goal.
Forest had two further chances before the half-time whistle, Eastwood saving well to deny Jamie Mackie, Grant Hanley doing well to block a Paterson shot.
The half-time whistle left plenty for Rovers to do, and plenty for Bowyer to ponder.
The much maligned officials were last out as the second half eventually got under way, neither side making a change at the break.
Almost immediately Rovers threatened. A Tom Cairney free-kick into the box was headed back across goal by Scott Dann, Tommy Spurr diverted the ball goalwards but Forest 'keeper Karl Darlow somehow clawed the ball away from underneath his crossbar.
The resulting corner kick also saw Spurr threaten, but from ten yards out the defender headed over.
Josh King replaced Lee Williamson on 54 minutes, four later Jordan Rhodes was introduced at the expense of Rudy Gestede.
However it was the home side who started to force the pace once more. Gonzalo Jera had served notice with a bouncing shot that flashed wide before Henri Lansbury, searching for his hat-trick, was denied by Simon Eastwood.
A handful of Tommy Spurr long throws allowed Rovers to build a spell of pressure. After one such throw Josh King broke through but was denied by Darlow, Cairney over with the rebound. Moments later Grant Hanley headed into the arms of the Forest 'keeper.
But with Rovers pressing they were caught by a sucker punch of a third Forest goal against the run of play. Quick feet by Jamie Paterson saw the midfield create space in the penalty area and he made no mistake with a lot shot into the far corner.
Forest brought on Guy Moussi and Matt Derbyshire, whilst Rovers David Dunn in an attempt to force a way back into the match.
The Rovers bench became more and more frustrated as time wore on, decision after decision going against the blue and whites. One such talking point was an altercation between Scott Dann and Darius Henderson with the Forest man appearing to punch the Rovers captain. After a period of treatment, Dann made his way down the tunnel, unable to continue.
That meant Rovers had to play the last five minutes a man shy and to their credit they continued to look for more goals, they saw plenty of the ball but were unable to make their possession count.
In contrast, Forest were decisive, Andy Reid letting fly with seconds remaining to add a fourth in added to time to ensure a miserable afternoon in the east midlands.
So after a busy week of football, Rovers return to action next Saturday at Ewood Park when Derby County are the visitors.
FOREST: Darlow, Harding, Collins, Lansbury, Reid (c), Mackie (sub Derbyshire 73 mins), Halford, Jara, Paterson, Vaughan (sub Moussi 74 mins), Cox (sub Henderson 79 mins).
Subs not used: de Vries (GK), Miller, Majewski, Abdoun.
Goals: Lansbury (pens) 15, 34 mins, Paterson 72 mins, Reid 90+5 mins.
Booked: Harding, Lansbury.
ROVERS: Eastwood, Henley, Dann (c), Hanley, Spurr, Williamson (sub King 54 mins), Lowe, Cairney, Taylor (sub Dunn 74 mins), Marshall, Gestede (sub Rhodes 58 mins).
Subs not used: Kean (GK), Kilgallon, Morris, Goodwillie.
Goals: Marshall 37 mins.
Booked: Taylor, Hanley.
Attendance: 22,456 (including 1367 Rovers fans)