Khalifa said that although Bordeaux have a chance with just one goal in the tie, they should have registered an away goal with the chances that they created.
"It's a shame not to have scored an away goal, because we had the chances," UEFA.com quotes Ben Khalfallah as saying. "It was a fairly even game and we matched Benfica well.
"I think we deserved better than 1-0 and on top of that they scored a lucky goal, but there's still hope for the return match and we'll try to qualify at home.
"We just lacked a clinical edge in front of goal, and didn't make the most of dead balls."
The Tunisian has made 23 appearances for Bordeaux this season.