With seconds remaining in the first half, the Chilean picked up a loose ball on the right flank and coolly slotted under Besiktas keeper Tolga Zengin.
The goal came in the 136th minute of the two-legged tie, giving the Gunners the upper hand for qualification to the competition proper.
Arsenal went on to win the tie (1-0 on aggregate) despite going down to ten men after Mathieu Debuchy's second bookable offense.
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