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Arsenal left back Gael Clichy headed into his own net in the 70th minute to give Villa the lead. Villa striker Ashley Young bent the ball into the area for Agbonlahor, but Clichy was under pressure and futilely tried to head the ball out.
Agbonlahor then made a strong run in the 80th minute and fired a right-footed shot past Arsenal goalkeeper Manuel Almunia.
Young could have given Villa the lead in the first half, but missed a penalty in the 20th.
Aston Villa's last league win against Arsenal came at Villa Park on Dec. 13, 1998 in a match that ended 3-2. Villa and Arsenal both have 23 points, with the Gunners ahead in fourth place on goal difference. It was a huge letdown for Arsenal, who beat Manchester United 2-1 last week and looked to keep the momentum to keep pace with league leaders Chelsea and Liverpool.
But now United jumped above Arsenal into third place with a game in hand after a 5-0 victory over Stoke. Arsenal's title hopes appear to be fading quickly - the Gunners are now nine points behind Liverpool, which have 32 points after a 2-0 victory over Bolton.
In the 20th minute, Almunia went the right way and saved Young's penalty after Theo Walcott brought down the winger in the penalty area. Arsenal defender William Gallas hacked the ball clear after Young scrambled to get to the rebound.
Gareth Barry, who is Villa's normal penalty-taker, was injured in the play that led up to the penalty, so Young went up to the spot.
It was a busy first half for Almunia, who started in goal after recovering from a head injury sustained last week in the United match. He had little time to settle after Young fired a shot straight at the Spaniard after just 17 seconds.
Almunia was also kept busy just after the half-hour mark, as Agbonlahor burst down the left and weaved into the area to the byline before crossing a ball into empty space in front of goal to Barry, who fired straight at the goalkeeper. A few minutes earlier, Young had made a strong run and fired a shot from about 35 yards that went just left of the goal.
Arsenal had few chances in the first half because of strong defending by Villa and the Gunners' midfield play was frequently broken up. The home side's best first-half chance came in the fifth minute when a Denilson through ball found Walcott, who made a good run but before sending a pass across goal that could not be met by Nicklas Bendtner. Cesc Fabregas later curled into the box, but Villa goalkeeper Brad Friedel collected the ball easily.
Arsenal manager Arsene Wenger kept the same side that defeated United, sticking to a 4-5-1 formation with midfielder Abou Diaby playing behind lone striker Nicklas Bendtner. But he gave up on that in the 61st minute and tried to add more pace to the attack by bringing on Emmanuel Adebayor for Diaby, and then Carlos Vela seven minutes later. Adebayor was back from an ankle injury picked up in Arsenal's loss to Stoke on Nov. 1.
Arsenal had a few chances in the second half. Fabregas' shot in the 84th was saved by Friedel, who also saved a couple of shots from Adebayor.
Villa manager Martin O'Neill made two changes to the side that lost 2-1 to Middlesbrough last week. Midfielder Stiliyan Petrov, who had missed the last three games with a hamstring injury, and right-back Luke Young, who recovered from a thigh problem, returned to action.
Arsenal was without Robin van Persie, who served out the second game of a three-match suspension.
Friedel made his 165th consecutive Premier League appearance and he needs only two more to surpass the total of 166 set by goalkeeper David James for Manchester City and Portsmouth between January 2004 and April 2008. Friedel's run began at the start of the 2004-2005 season with Blackburn, which he left at the end of last season to join Villa. The American would reach 167 against Fulham at Craven Cottage on November 29.