© AP Photos
The visitors started brightly, with Papiss Cisse wasting an early chance to put the Magpies ahead when he miscued his shot following a fast counter-attack.
However, Cisse made no mistake with his second chance of the night, finishing well from Moussa Sissoko's expertly delivered cross into the area.
Newcastle continued to threaten, with Cisse striking the post midway through the first half but Benfica grew in confidence as the game progressed.
Benfica took control of the match in the second half and should have been ahead when Rodrigo picked out Cardozo but the striker lacked composure and drilled his shot wide.
However, the home crowd were not made to wait long to celebrate a second goal, with Davide Santon's poor back pass allowing Lima to slot the ball past Krul.
The first leg result was put beyond doubt in the 71st minute when Steven Taylor was adjudged to have handled inside the area to give Cardozo the opportunity to score from the penalty spot at the second time of asking.
Benfica finished the game impressively, with Nicolas Gaitan stinging Tim Krul's palms in the final stages as Newcastle held on to prevent further damage.