Eduardo put Arsenal ahead with a smart finish in the 11th minute, chesting a fine cross down before sidestepping keeper Andres Palop and poking home.
But Seydou Keita's bullet from the edge of the area leveled the score line in the 24th minute.
Ten minutes later, Luis Fabiano towered to meet a cross from the right-hand side and his header floated past the stretched Manuel Almunia.
Frederic Kanoute was fouled by Kolo Toure in the area one minute from time and the Mali striker stepped up to slam the resulted penalty home.
The URFA cup holders now top the group with 12 points, two ahead of Arsenal. Both teams secured their spots in the knock-out stage.
In the same group, Slavia Prague snatched a precious point from Steaua Bucharest to grab a UEFA Cup spot, holding the hosts to a 1-1 draw.
Zdenek Senkerik scored in the 78th minute to cancel out a Valentin Badea opener in the 12th minute.
Slavia guaranteed third place with five points, four ahead of rooted Steaua, with one match to go.