Brazilian forward Lima opened the scoring just after the hour mark against the sixth-placed visitors, who defended stoically against a Benfica side that have lost just once in the league all season.
Enzo Perez converted from the penalty spot with 20 minutes remaining and the result was put beyond all doubt when Eduardo Salvio notched his fifth of the campaign in the 83rd minute.
Jorge Jesus' side are now three points clear of rivals Porto, who matched Benfica with a convincing 3-0 triumph at Academica.
Jackson Martinez grabbed two goals in 11 first-half minutes to put Julen Lopetegui's side comfortably ahead going into the interval, with Hector Herrera bagging a third two minutes after the restart as Porto remain unbeaten in the league this term.
Estoril made it four games unbeaten as they overcame Vitoria Setubal thanks to Kuca's first-half effort, while Rio Ave played out a goalless stalemate with Gil Vicente.
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