The Hoops now need to take more points than Benfica from their final Group G game if they are to qualify, although they host Spartak Moscow and the Portuguese side travel to Barcelona.
Samaras' header from Charlie Mulgrew's corner cancelled out Ola John's early opener for Benfica but Ezequiel Garay sealed the win for the dominant hosts in the 71st minute.
"For the full 90 minutes we were a little bit nervous," said Samaras. "We didn't have a clear mind but it's finished.
"I didn't think we played really well but the game was really close. The only thing we can keep is the team effort and the really hard work we had.
"We are just looking forward to the next game and we must stay positive.
"We still have a chance to go through and we will do our best to go through to the next round."
Influential midfielder Victor Wanyama will be suspended for the home game against Spartak after picking up a late yellow card.
Samaras added: "Victor's a great player and he is helping the team a lot with his strength. But I think we have enough players in the squad to cover him."