Goals from Alexis Sanchez and Cesc Fabregas did the job for Tito Vilanova's side who lost captain Carles Puyol to a suspected broken arm and defender Sergio Busquets to a red card late but it had no effect on the outcome.
It took the away side just six minutes to open the scoring with Lionel Messi playing a smart one-two with Jordi Alba before fizzing a low ball into the six-yard box for Alexis Sanchez to slot home for his first goal of the season.
The Spanish giants began to dictate the tempo of the match and nearly added a second on 21 minutes, Alexis causing the Portuguese champions all kinds of problems down the left-hand side before teeing up Messi, who would have scored had it not been for a stunning one handed save from Porto gloveman Artur Moraes.
Benfica have now not won in 13 encounters with Spanish teams and nearly found themselves down a second straight after the restart with Fabregas slotting through to Alexis who clipped the left upright with the keeper well beaten.
The game was all but won after Messi grabbed his second assist of the game, an unstoppable run that committed five defenders before laying on Fabregas who drilled home at the near post.
The Estadio da Luz was silenced on 78 minutes, due to horror injury to Barcelona's skipper Puyol with what looks to be a broken arm. The injury makes it almost certain he will miss the upcoming El Clasico with Real Madrid.
Another player that will be missing for Barcelona for their next Champions League fixture against Celtic will be Busquets who got sent off just before the final whistle for a raised arm on Benfica skipper Maxi Pereira.
Barca now have secured six points from two Champions League outings following their come-from-behind 3-2 win over Spartak Moscow two weeks ago as Benfica have failed to score with just a single point which stemmed from their 0-0 draw at Celtic.
2012/13 UEFA Champions League - Group G
Estadio da Luz, Lisbon, Portugal - 63,847