Goalkeeper Lucasz Fabianski's vulnerability in the air was exposed on a number of occasions before Rovers captain Chris Samba took advantage to head home a 69th-minute winner.
Robin van Persie's first goal since October 31, having been sidelined for five months with an ankle injury, had put the Gunners ahead early in the first half only for David Dunn to equalise from close range just before the interval.
Arsenal, who have still to guarantee third place in the table, had endured some physical battles on this ground over the years but this was not one of them.
Set-pieces from both sides dominated in the opening 45 minutes but once Blackburn sensed their opportunity they seized it and could easily have been awarded a penalty early in the second half for Sol Campbell's clumsy challenge on Morten Gamst Pedersen.
Their tactic of packing the penalty area with bodies and virtually surrounding Fabianski every time there was a chance to get the ball into the box was one the Poland international struggled to cope with.
Fabianski was deputising for the injured Manuel Almunia, not immune to the odd error himself, but his performance did little to instil confidence in his defence.
But there was an air of casualness about the Gunners as early as the third minute when forward Carlos Vela gave an indication of why this was his first Barclays Premier League start in a year and a day.
Ryan Nelsen failed to cut out the through-ball meant for Theo Walcott but with goalkeeper Paul Robinson's indecision keeping him rooted to his line the England winger was able to collect and cross only for the Mexico international to sidefoot wide of an empty goal.
Three minutes later Blackburn's threat from set-pieces was illustrated as Pedersen's 25-yard free-kick had Fabianski diving to his right to save well.
But it was a dead-ball delivery by Arsenal's Samir Nasri in the 14th minute which produced the opening goal.
Bacary Sagna flicked on at the near post and Van Persie was on hand to head in his eighth goal in eight matches against Rovers - more than he has scored against any other Premier League club.
The Holland international then forced Robinson into a low save to his right from a 25-yard free-kick on the half-hour.
Set-pieces continued to provide the best chances and Fabianksi, who did not look comfortable under pressure, had to tip over another Pedersen free-kick.
Three minutes before half-time another corner brought a goal, this time an equaliser for Rovers.
Pedersen's left-wing corner dropped to Nelsen who rolled a pass to Keith Andrews on the right of the penalty area and his driven cross deflected off striker Jason Roberts to Dunn who tapped home at the far post.
Four minutes after half-time Pedersen's miss from a one-on-one with Fabianski was ruled academic by an offside flag.
The Norway international had run from deep to collect Dunn's pass through the middle of Arsenal's defence but he overhit his lob and the ball landed on top of the net.
Within five minutes Pedersen had a chance to redeem himself from Andrews' dinked pass but shot too close to Fabianski.
As he tried to reach the rebound he was felled by a clumsy challenge from Campbell but referee Martin Atkinson awarded only a corner.
On the hour substitute Junior Hoilett's first touch having replaced Grella saw him fire in a shot destined for the top corner which Fabianski palmed behind.
Wenger sent on Andrey Arshavin, making his first appearance since the end of March after a calf problem, for Vela but before the Russian had chance to get involved Blackburn took the lead.
Pedersen's corner was drilled into the six-yard area and Fabianski came but failed to connect, allowing Samba to head in from three yards out.
Wenger sent on Eduardo for Eboue in an attempt to get the equaliser but Allardyce responded by taking off playmaker Dunn and sending on centre-back Phil Jones to shore up the defence in a five-man backline.
Rovers held on for four minutes of added time to move up to 10th in the table and sign off with an impressive record at Ewood Park, where they have lost only three times.