Arsene Wenger's 'reserves' came out of the blocks fast to take the lead within five minutes.
A series of clever wall-passes with 18-year-old Mark Randall, making his first appearance of the season, allowed Nicklas Bendtner to create space and float a pinpoint cross over Blackburn's static back line.
Lurking beyond, Diaby coolly steered the ball high into the net past Brad Friedel.
Largely chasing shadows and with cries of 'ole' from the visiting Arsenal fans ringing in their ears, Rovers did eventually apply some pressure.
David Dunn's 18-yard piledriver forced Arsenal Lukasz Fabianski into a strong-armed save.
But Arsenal's swagger redoubled.
Taking up possession in midfield, Denilson exchanged passes with Randall and played a long, searching ball behind the Rovers defence.
Confused by Eduardo's run behind him, Samba missed a chance to cut out the ball allowing the Croatian striker to coolly slot past a furious Friedel.
Minutes before half-time Blackburn managed to pull a goal back.
Matt Derbyshire fired a dangerous ball across the area which the onrushing Santa Cruz met with the outside of his right boot to give Blackburn hope.
Arsenal boss Arsene Wenger would have cause to complain as Derbyshire looked a shade offside but Blackburn manager Mark Hughes must have been the one raging at half-time.
Santa Cruz scored two goals to bring Blackburn back into the match
His side duly came out fighting and with long-ball tactics bypassing Arsenal's mesmeric midfield, the Gunners started to look nervy.
On the hour, Bentley bent a vicious dead ball into the box for Santa Cruz to rise highest and draw Blackburn level - his fifth goal in two games.
Arsenal struggled to regain the initiative and Alexandre Song, at the centre of most of the rearguard action, made a hash of a clearance near his own goal with the ball deflecting to Derbyshire who narrowly shot wide.
With both players pushing for victory, Santa Cruz missed a glorious chance to put Blackburn through by swiping at the ball as it dropped inside the box.
Referee Mike Riley sent Denilson off in stoppage time for a dangerous two-footed challenge on David Dunn which triggered a melee between both teams.
The fast and furious pace relented in extra time with Blackburn just egding possession.
But just before the teams swapped ends, Arsenal centre back Song marched through the centre of the pitch to release Eduardo.
Holding off Ryan Nelsen's challenge, his first touch was immaculate, allowing him to race into the box and calmly stroke the ball past Friedel's outstreched palm to seal Arsenal's progress.
Blackburn: Friedel, Reid, Samba, Nelsen, Warnock (Khizanishvili 120), Bentley, Savage, Dunn (Mokoena 105), Pedersen, Santa Cruz, Derbyshire (McCarthy 90). Subs Not Used: Brown, Roberts.
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Interview: Arsenal manager Arsene Wenger
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