The 30-year-old Brazilian, a little-known journeyman until he joined Benfica two years ago, broke the deadlock in the 57th minute and added a second goal three minutes later helped by a blunder from goalkeeper Vid Belec.
Benfica's 11th successive league win gave them an unassailable seven-point lead over second-placed Sporting with two games to play.
Although Benfica are Portugal's most successful club with a record 33 league titles, it was only their third in 20 seasons after falling into the shadows of arch-rivals Porto.
Benfica, looking decidedly jittery, missed a flurry of early chances.
Rodrigo side-footed weakly at Belec when he seemed certain to score in the sixth minute and squandered another chance four minutes later when he fired wildly over from an excellent position.
Olhanense grew in confidence and held out until Belec only partially stopped Nicolas Gaitan's low shot and Lima snapped up the rebound.
Three minutes later Lima burst down the right and a seemingly harmless shot squirmed through Belec's legs.
Sporting, who won 1-0 at Belenenses on Saturday, are guaranteed second spot and a place in the Champions League group stage next season.
Porto, champions 14 times in the last 20 seasons, need to beat Rio Ave on Monday to make sure of third position and a slot in the Champions League qualifying rounds next season.
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