Rovers' Under-21s lost their first match at Leigh Sports Village this season as Arsenal ran out worthy winners.
The Gunners were the better of the two hardworking young sides, as they scored twice in the first half and added a third early in the second half.
Defending from corners was Rovers' achilles heel in the first half as Semi Ajayi and Daniel Boateng scored.
Early in the second Chuba Akpom added Arsenal's third, and although Rovers battled hard for a way back into the game, the visitors were able to see out the game.
At a windy Leigh Sports Village it was the visitors who dominated the first 45.
They set the tone early when Ainsley Maitland-Niles blocked a Bradley Bauress clearance to race into the area to tee up Thomas Eisfeld but the German blazed over the bar.
Steve Gatting's side were dominating midfield and that allowed pressure to build, eventually it told from an 18th minute corner kick as Kris Olsson sent the ball over from the left and it was flicked on to trialist Oluwasemilogo Ajayi who buried the ball in at the back post.
Five minutes later and Rovers had a chance from a corner of their own. Raheem Hanley's ball found Anthony O'Connor who headed goalwards but it was cleared off the line, the ball was worked as far as Hugo Fernandez but his curling shot was never troubling the Arsenal goal.
On 25 Rovers broke well from an Arsenal attack through Tim Payne and Devarn Green, Raheem Hanley teed up Fernandez but Deyan Iliev in the Arsenal goal saved one-handed low to his right.
They were the only two opportunities for Rovers as the visitors enjoyed the better of the play in the final 15 minutes of the half. Eisfeld seeing a shot saved low by Raya before defender Isaac Hayden had all the time in the world to shoot from outside his area, the ball deflecting just wide.
Another Arsenal break down the right saw Eisfeld find Daniel Boateng on the overlap, with the full-back seeing his near-post shot tipped behind for a corner.
Olsson delivered from the right and as David Raya was left in no-mans land, Boateng rose highest to head home to increase Arsenal's lead.
The Gunners had two further chances to add to their goal tally as the half drew to a close, Chuba Akpom closed down a Raya clearance only to see the ball rebound over the bar, before Maitland-Niles fizzed an 18-yard effort narrowly over.
The start of the second half saw Rovers dealt an double blow.
Firstly Tim Payne picked up an ankle injury and had to be helped from the field. Then as the home side were re-adjusting with Deniz Pero coming on, the Gunners took full advantage to score their third of the night.
Chuba Akpom exchanged passes with Maitland-Niles before skipping past the challenges to score sweetly beyond Raya.
Despite the scoreline it was to Rovers credit that Eric Kinder's young side kept pushing for a way back into the game.
Devarn Green almost connected with a cross from Bradley Bauress, whilst Paulo Jorge was wide with a volley.
Then Hugo Fernandez opted to shoot at goal with a 20-yard free-kick, the ball watched wide of his near post by Iliev.
There was still time for Rovers to give an Under-21 debut for Academy striker Dean Rittenberg, but with three goals inside the first 50 minutes from Arsenal the damage was already done and the Londoners were able to see the game out comfortably.
Rovers are back at Leigh Sports Village on Monday September 16th when Stoke City are the visitors.
ROVERS: Raya, Daly, Bauress, Paulo Jorge, Tumwa, O'Connor, Fernandez, Payne (sub Pero 48 mins), Preston (sub Doyle 46 mins), Green (sub Rittenberg 88 mins), R. Hanley.
Subs not used: Urwin, Vicars.
ARSENAL: Iliev, Boateng, Siemann, Kamara, Hayden, Ajayi, Maitland-Niles, Olsson, Akpom, Eisfeld.
Subs not used: Jebb, Vickers, Lipman, O'Connor, Fagan.
Goals: Ajayi 18 mins, Boateng 36 mins, Akpom 49 mins.