The hosts largely dominated the first half hour and opened the scoring in the 35th minute when goalkeeper Pedro Trigueira brought down Nicolas Gaitan in the area, even though the Argentine forward appeared to be chasing a lost cause.
Jonas sent Trigueira the wrong way from the spot, before converting a second penalty in the 69th minute, his 10th goal of the season, after Richard Ofori handled.
Sanches added a spectacular third in the 85th minute, which drew praise from coach Rui Vitoria.
"(Sanches's goal) was the icing on the cake," Vitoria told Record. "It was a wonderful goal from a young man who is growing.
"We will never forget this first big goal. We are delighted for him and proud."
Benfica remain in third following their victory, having picked up 24 points from their opening 11 matches.
They are three points behind second-placed FC Porto, who host Pacos de Ferreira on Saturday, and five behind leaders Sporting Lisbon who visit Maritimo.
Academica are second from bottom on seven points, having gone five games without a win.
(Editing by Greg Stutchbury)
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