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The visitors were the first to trouble the goal when Bryan Ruiz collected on the edge of the area and let fly. The Costa Rican's effort took a deflection and span just wide of the post.
Arsene Wenger's men were unable to maintain the two-goal advantage as Ruiz's corner was headed low into the net by Dimitar Berbatov six minutes later.
Fulham got back on level terms five minutes before the interval when substitute Alexander Kacaniklic, who had come on for the injured Kieran Richardson, met Berbatov's cross with a header into the corner.