Liverpool took the lead through Daniel Agger after nine minutes at the Estadio da Luz but had Ryan Babel harshly sent off before the interval and then conceded two penalties after the break, both converted by Oscar Cardozo.
NEWS:Cardozo pens sink Liverpool
"To concede two goals to two penalties and have one goal disallowed is disappointing, but still it is a good result," Benitez told the club's website.
"I have confidence we can do well and it will be totally different at Anfield. With the fans behind us, we can score goals and progress."
Benitez was surprised by referee Jonas Eriksson's decison to send off Babel, who appeared to do little more than put his hand on the face of Benfica defender Luisao in a melee after he had brought down Fernando Torres.
"I was surprised because a foul from behind is more serious for me," Benitez said. "It's difficult to understand and impossible to change so we have to move forward and think about Anfield and our fans behind the team.
"Always when decisions are made against your team, you don't like it. But you cannot change it and the only way now is to try to be positive and think about our fans behind the team and playing with 12 men at Anfield."
Liverpool will host the second leg on April 8.
