Two classy strikes either side of half time saw the Blues lose their first summer outing at Shawbridge.
A stunning overhead kick from Stefan Mols and a thumping Jack Vale finish gave a youthful Rovers’ Under-23 side victory in their opening pre-season fixture.
But Clitheroe never made it easy for the visitors on an encouraging night for Phil Brown’s new-look side.
The Blues’ boss took the opportunity to use most of the players he currently has available, as well as run the rule over a couple of trialists.
And despite some way to in terms of reaching match sharpness, he was rewarded with hard-working performance in front of an excellent gate of 327.
New signing Elliot Pond had the chance to give the Blues the lead but failed to cap a lively performance with a goal as his first-half penalty was saved.
And 10 minutes later Rovers took the lead when Spanish midfielder Mols found the bottom corner with an acrobatic overhead kick.
Blackburn – who used mainly youth-team players – had threatened early on through Luke Brennan and Chanka Zimba.
But they were both denied by former Clarets’ youngster Connor King, who made two smart saves at the start of a tidy opening half before making way for Cameron Terry at the break.
Wideman Conor Gaul and Terry Cummings stretched the Rovers’ defence as the Blues hit back with Cummings a real handful on his first home outing since signing from Burscough.
And when Pond was tripped in the box, only a fine Jordan Eastham save from the striker’s spot-kick denied the Blues the lead.
Brown made a number of changes at the break and within two minutes of the re-start Rovers had doubled their lead through Vale’s impressive strike as the Wales youth international picked out the top corner.
But the Blues refused to buckle and had chances themselves in the last half hour.
Substitute Jordan Darr twice went close, while teenager Jake Connelly was only denied his first goal in a Clitheroe shirt by a goalline clearance as Clitheroe’s pre-season preparations went up a notch.
Brown’s side plays their next game at Charnock Richard on Saturday with their opening competitive game in the FA Cup just three weeks away.
Clitheroe starting XI: King; Trialist, Trialist, Dugdale, Lonsdale; Cummings, Trialist, Russell, Gail; Pond, Gregory.
Second half XI: Terry; J. Gregory, Trialist, Muir, Trialist; Cummings (Price), Stanley (Clegg), Trialist, Connelly; Darr, Tanner.
Rovers starting XI: Eastham, Jackson, Whitehall, Annesley, Pike, Durrant, Lyons, Saadi, Brennan, Mols, Zimba.
Blackburn: Eastham, Jackson (Boyomo 46), Whitehall, Annesley, Pike, Durrant (Burns 33), Lyons (Saadi 61), Saadi (Connolly 33), Brennan (Garrett 63), Mols (Durrant 61), Zimba (Vale 46).