Argentine superstar Lionel Messi remains one goal away from equalling Gerd Muller's scoring record after being introduced as substitute just before the hour.
But more worryingly for the Catalan giants he was carried off on a stretcher close to the end of the Group G encounter.
That was not the only late drama as Celtic, who had to better Benfica's result to reach the last 16, secured a 2-1 victory over Spartak Moscow to condemn Jorge Jesus' side to a place in the Europa League.
Much of the pre-match build-up had focused on Messi, with the prolific Argentina forward just one strike away from matching Germany legend Muller's 1972 mark of 85 goals in a calendar year.
But the three-time Ballon d'Or winner was named on the bench in Tito Vilanova's much-changed line-up which included eight B team players.
Barca had the bulk of possession but it was the visitors who posed the greater threat in the first half.
Benfica had 11 attempts, six of which were on target, but failed to find a way past Jose Pinto.
Rodrigo slotted a left-footed shot just wide, before Lima's diving header whistled past the near post.
Barcelona's best chance saw Rafinha's angled effort headed off the Benfica line.
The hosts looked brighter after half-time, but the biggest cheer of the night greeted the 58th-minute introduction of Messi.
His curling free-kick was well-held by Benfica keeper Artur before Messi pulled up clutching the back of his leg.
Benfica knew they needed a goal to advance at the expense of Celtic and spurned late chances through substitute Oscar Cardozo and Maxi Pereira.