Albrighton's milestone effort came nine minutes into the second half after a mistake by Gunners defender Thomas Vermaelen.
Arsenal striker Robin van Persie had equalled Thierry Henry's club record of 34 for the most Premier League goals in a calendar year before Benayoun's 87th minute decider.
Villa defender Alan Hutton was sent off in injury-time for two bookable offences.
Villa have donated the 20,000 cheque from Barclays for the 20,000th goal to their official charity partner, the Acorns children's hospice.
The result was harsh for Alex McLeish's side, who produced their best home performance of the campaign, with Charles N'Zogbia having one of his more influential games.
But their inability to defend set pieces proved costly as Benayoun headed in a corner from Van Persie as Arsenal moved level on points with fifth placed Chelsea.
The home side were the first to threaten and it needed a fine save from Wojciech Szczesny to prevent Gabriel Agbonlahor giving them a sixth-minute lead.
N'Zogbia floated the ball in the Gunners box after a one-two with Marc Albrighton and Agbonlahor's header from close range was parried by Szczesny.
Villa looked more aggressive and committed than against Liverpool at the weekend
N'Zogbia was looking lively and got the better of Francis Coquelin before delivering a cross to the near post.
Agbonlahor was first to react but Aaron Ramsey got in an important block.
It was against the run of play when Van Persie put Arsenal ahead.
Clark tugged at the short of Theo Walcott inside the box and referee Jonathan Moss pointed to the penalty spot.
Up stepped Van Persie to hammer the spot kick into the roof of the net.
Walcott could have made it 2-0 after running onto Van Persie's pass.
But Brad Guzan was alert and raced out of his box to block the shot with his chest.
N'Zogbia was having one of his best games for Villa and he nutmegged Coquelin before sending him a teasing cross which eluded everyone.
Coquelin became the first player to be yellow carded after 28 minutes for a mis-timed challenge on N'Zogbia.
Ramsay should have done better in an Arsenal counter-attack when he shot well wide after a Van Persie flick on.
Clark was booked after 38 minutes for a foul on Mikel Arteta and then Per Mertesacker was yellow carded for checking the run of N'Zogbia.
Villa continued to do most of the pressing at the start of the second period.
Szczesny was forced into a hurried clearance under pressure from Albrighton.
When Arsenal counter-attacked Per Mertesacker failed to make proper contact on his shot from a Walcott cross.
But after 54 minutes a mistake by Vermaelen allowed Albrighton to score the 20,000th goal since the Premier League began nearly 20 years ago.
The Villa winger kept his cool before sliding the ball wide of Szczesny.
Arsenal retaliated instantly and Guzan produced a superb save to deny Mertesacker in a counter-attack.
They forced a string of corners in quick succession but Villa held firm.
Van Persie was booked after 78 minutes for diving in the Villa box.
Dunne produced another vital interception to block a shot from Rosicky and substitute Andrey Arshavin had a shot deflected over the bar.
But then Benayoun broke Villa's hearts as he was left with a free header inside the box from Van Persie's corner.
Hutton was booked for a foul on Van Persie and then sent off in injury-time for a second yellow card offence on Vermaelen.