Nicolas Gaitan burst through the Astana defence to provide the breakthrough six minutes into the second half and Kostas Mitroglu made the points safe for the Eagles in front of a sparse crowd at the Stadium of Light.
But Astana, the first Kazakh team to reach the group stage, will have plenty of positives to reflect on as they make the 7,000 kilometre trip back to Central Asia.
The Kazakh champions kept Benfica at bay for the first 45 minute with some solid defending, plus two last-gasp saves by goalkeeper Nenad Eric who denied Jonas with his leg on both occasions.
In between, Benfica goalkeeper Julio Cesar give home fans the jitters as he fumbled Foxi Kethevoama's curling free kick before gathering the ball at the second attempt.
Astana nearly took a sensational lead at the start at the second half when Aleksei Schetkin, who had just come on as a substitute, got between Jardel and Luisao to poke an effort against Julio Cesar's post.
Gaitan ended their resistance when he latched onto a loose ball, powered his way through a gap between the defenders and placed an angled shot past Eric in the far corner.
Mitroglu, having headed wide from eight metres, atoned for the miss when he turned in Eliseu's cross from close range following another move down the left in the 62nd minute to secure the points for the Portuguese champions.
(Writing by Brian Homewood in Berne, edited by Mike Collett)
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