Djibril Cisse looked to be in an offside position as Fowler bagged his third goal in as many games.
The European Champions snuffed out the threat of the in-form Craig Bellamy, as Mark Hughes' side slipped to their first home defeat in 13 games.
With Turkish playmaker Tugay still sidelined with a calf injury, Hughes named an unchanged side following last weekend's 2-2 draw at Portsmouth.
Steven Gerrard and Peter Crouch were the surprise absentees from the Liverpool squad, as Rafael Benitez clearly had one eye on next weekend's FA Cup semi-final.
Fernando Morientes partnered Fowler in attack, whilst Stephen Warnock and man of the match Mohamed Sissoko both returned to the starting line-up.
A minute's silence to mark the 17th anniversary of the Hillsborough disaster was impeccably observed, but as play got underway, both sides remained relatively flat-footed for the opening half an hour.
The game sprung into life however in controversial circumstance on 29 minutes.
John Arne Riise's long throw to Fowler was chested into the path of Morientes, but with Cisse standing five yards offside, play was allowed to continue and Morientes squared the ball back to Fowler, who slotted home with a crisp right foot shot.
As the half-time whistle approached, the visitors almost doubled their lead with a swift break.
After a brilliant tackle on Bellamy, Sami Hyypia's long ball to Morientes was headed down to Fowler. The Liverpool legend then played in Cisse with a ball over the top, but the Frenchman's well struck shot was brilliantly saved by Brad Friedel, with the ball bouncing up onto the bar and out for a corner.
Fresh from the break, Rovers looked more of an attacking threat in the second half. After skipping past three Liverpool defenders, David Bentley fired low across goal, only for Jose Reina to smother the ball with Morten Gamst Pedersen arriving at the back post.
On 51 minutes, an in-swinging Pedersen corner was headed inches wide of the far post by Ryan Nelsen and just 20 minutes later, Rovers almost pulled level with their best move of the game.
Steven Reid's long ball out to the left was headed into the centre by Pedersen, Bellamy played in Robbie Savage with a deft first touch, but the midfielder's left foot strike found the side netting.
Morientes headed wide just a minute later, before Cisse ought to have wrapped up the points in the 90th minute.
The former Auxerre striker was played clean through down the left and after former Liverpool keeper Friedel saved his initial effort, the big number nine struck the post with the goal at his mercy.