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Huerzeler, 31, has overseen two victories to keep Brighton provisionally top of the standings after two games
The Gunners produced a laboured display against the crafty south coast club and were outplayed after the break.
The defeat means it is now mathematically impossible for sixth-placed United to qualify for the Champions League, as they sit five points adrift of fourth-placed Arsenal with one game left to play.
Ronaldo, without a goal since December and dropped to the bench by interim manager Ralf Rangnick in some recent matches, answered his critics five minutes after half-time with a superb finish.
Brighton had taken the game to Chelsea in the first half but fell behind after a defensive blunder in the 23rd minute when goalkeeper Mat Ryan fouled Werner in the area and Jorginho coolly converted the penalty.
Arsenal, who fired Unai Emery as manager last week and appointed former player Freddie Ljungberg as caretaker boss, now sit 10th in the table on 19 points, with Brighton a single point behind and three places below them.
Results 1-6
