Kokcu prodded Alvaro Carreas' teasing delivery beyond Monaco goalkeeper Radoslaw Majecki to pinch the tie for his side. The Ligue 1 team had earlier fought back from two goals down to get level, before equalising again with nine minutes to play through George Ilenikhena, but were unable to hold on for extra time.
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Victory sees Benfica qualify for the last 16 of the Champions League for the third time in four seasons. The Portuguese side have only lost three of their 10 matches in the competition this season, two of which have come away to Bayern Munich and in a 5-4 thriller at home to Barcelona, while they have beaten Atletico Madrid 4-0 and Juventus 2-0.
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Bruno Lage's side have now guaranteed themselves a tie with either Liverpool or Barcelona in the last 16, which they will be underdogs to progress from but will fancy themselves to keep competitive at least.