McFarlane netted his side’s opener just before half-time, with Cooper finding the back of the net after 56 minutes with a fine free-kick.
Blues made a bright start and went close after just three minutes. Viv Solomon-Otabor threaded a neat ball through for Kyle McFarlane to run onto, but the Blues striker fired just inches wide of the post.
Their next opening came as a result of some neat inter-play on the right of the area which culminated in the ball finding its way to Josh Dacres-Cogley. Dacres Cogley evaded his marker before letting fly with a curling goalbound effort, but it was comfortably saved by Jake Turner.
Bolton should have taken the lead on the 12th minute following a corner. The ball was sent in deep by Jack Earing, where it was met by an unmarked Alex Honeyball. Fortunately for Blues, the Trotters captain headed just off target with the goal at his mercy.
With 22 on the clock Bolton keeper Turner was forced into action when he did well to save Solomon-Otabor’s strong low show with his feet.
But it was not all one-way traffic and Blues keeper Connal Trueman had to be alert to rush out and grab the ball off the feet of Alex Samizadeh when a long ball over the top wrong-footed the Blues defence.
With just three minutes to go before the break, Blues finally got the goal that their positive play deserved when McFarlane fired his side in front following a Charlie Cooper corner.
Cooper sent the ball into the near post where it was scuffed by a Bolton defender into McFarlane’s path. The striker’s first attempt was blocked, but he made no mistake as it fell to him a second time and he lashed the ball home.
Half-time:Blues Under-23s 1 Bolton Wanderers Under-23s 0
Blues began the second-half in the positive vein they had finished the first and three minutes in Reece Brown saw his deflected shot from the edge of the box saved low down by Turner.
Blues found themselves 2-0 in front just before the hour-mark after winning a free-kick right on the edge of the box.
Cooper stepped up and fired home an unstoppable effort which left the Bolton keeper with no chance as it hit the back of the net.
Buoyed by their two-goal advantage Blues began to pile on the pressure.
Reece Brown lashed a shot over the bar for the hosts, before Bolton striker George Newell shot just over from close range.
Blues had a late shout for a penalty after McFarlane went over in the box under a challenge from a Bolton defender, whilst McFarlane required several minutes of treatment before eventually retiring from the action to be replaced by George O’Neill. And to compound matters Blues were only awarded a corner.
With just three minutes remaining of regular time Blues had a chance to extend their lead when Brown’s pass found Dacres-Cogley inside the area, but his attempt on goal was well blocked by a defender
Full-time: Blues Under-23s 2 Bolton Wanderers Under-23s 0
Blues Under-23s: Jake Weaver, Paul Caddis, Steve Seddon, Luke Maxwell (Noe Baba, 76), Daniel Cleary, Josh Martin, Josh Dacres-Cogley, Charlie Cooper, Kyle McFarlane (George O’Neill, 82), Reece Brown, Viv Solomon-Otabor.
Subs (not used): Connal Trueman, Wes McDonald, Beryly Lubala.
Goals: McFarlane 43, Cooper 56
Bolton Under-23s: Jake Turner, Callum Spooner, Cole Lonsdale, Alex Honeyball, Sam Lavelle, Alex Perry, Hyuga Tanner, Jake Earing, George Newell, Darren McKnight (Matthew Fearnley, 53), Alex Samizadeh.
Subs (not used): James Aspinall, Harry Brockbank, Matthew marsh, Josh O'Hanlon.
Bookings: Honeyball (87)