Oscar Cardozo broke the deadlock for the visitors after 34 minutes, the Paraguayan sending a low drive beyond Ricardo.
Jorge Jesus' men were soon two up as Marcelo Goiano inadvertently headed into his own net from a Nicolas Gaitan cross.
Forward Lazar Markovic put the result beyond doubt in the 87th minute, prodding home from close range after a Ruben Amorim pass.
Despite enjoying their fair share of attempts at goal and possession, Academica struggled to make an impact in the final third as they fell to a fifth defeat this season.
The win lifts Benfica into second above Sporting Lisbon, who face Maritimo on Saturday.
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