A brace of penalties from Oscar Cardozo cancelled out Daniel Agger's early opener with the visitors playing over an hour with ten-men after Ryan Babel's dismissal.
Both sides started tentatively as they looked for early possession, but it was Rafael Benitez's men that took the lead with the first real attack.
A quick free-kick from the hosts was intercepted by the Reds and played to Steven Gerrard on the left wing.
The Liverpool skipper's fine control and infield dart was unceremoniously halted by Victor Pereira and Daniel Agger's clever finish from the resulting set-piece opened the scoring inside ten minutes.
Central-defender Agger met the ball perfectly with a deft back-heel, diverting the ball beyond the flat-footed Julio Cesar in the Benfica goal.
Within three minutes, Benfica star-man Cardozo sensationally scooped over from six-yards.
A telling left-wing cross evaded the Liverpool back four, but the in-form Paraguayan couldn't restore parity when he really should have.
Argentine duo Angel Di Maria and Pablo Aimar combined well in spells as they threatened Jamie Carragher and company, but the final ball was lacking.
Alexandre Fabio Coentrao's fine centre from the left soon after landed straight onto Santos Ramires' head, but he missed the target when well placed.
Di Maria went close himself with a rasping left-footed drive that crept over Pepe Reina's bar as they continued to force the issue.
The game burst into life as Luisao's swipe on Fernando Torres brought the first yellow card of the night on the half hour.
A heated exchange followed and Liverpool winger Ryan Babel was dismissed by referee Jonas Eriksson for raising his hands to the Brazilian defender.
The man advantage saw Benfica take the game to their opponents and Di Maria flashed wide before David Luiz picked up a cheap booking for kicking the ball away.
From the free-kick, Liverpool had the ball in the net again, but the linesman's flag came to Benfica's rescue.
Torres struck home after Julio Cesar made a hash of his punched clearance, but in the lead up to his effort, Dirk Kuyt had strayed marginally offside.
Javier Garcia then went close, turning a long throw onto the roof of the net before Emiliano Insua went into the busy referee's book for pulling back Aimar, meaning he will miss the return leg at Anfield through suspension.
Further Benfica pressure followed, but Rafael Benitez's men clung on as they went in a goal to the good at half-time.
The second period started as the first ended with Benfica on top.
Cardozo headed straight at Reina and Aimar went down in a heap, but his hopeful penalty appeal was turned down.
It was Cardozo who missed another gilt edged chance, nodding over inside the six-yard box from Di Maria's corner when unmarked, but Benfica finally grabbed a deserved equaliser from the penalty spot on the hour mark.
Cardozo made up for his succession of sitters as he smashed home from the spot after Insua tripped Aimar following a Di Maria free-kick that crashed against the post.
Veteran striker Nuno Gomes entered the fray at full-back Pereira's expense as Benfica chased a first leg advantage.
A rare chance fell Liverpool's way with 20 minutes to go as Gerrard's near post free-kick was headed over from Torres, who cut a forlorn figure as the lone front man.
Reina's name was taken by referee Eriksson for time wasting before Torres missed a golden opportunity to regain the lead.
A Liverpool counter-attack left their star-man with a clear run on goal after Kuyt's through ball, but his usual calmness deserted him as he screwed wide.
The game took another twist as the hosts finally went into the lead.
Di Maria's cross on the left struck Carragher on the arm and after consulting his assistant, referee Eriksson awarded a second penalty.
Carragher was booked and Cardozo slotted home again amid scenes of delirium in the stands.
Benfica huffed and puffed and, with a free-kick in dangerous territory for the hosts deep into injury time, Di Maria wasted the opportunity as the referee ended the heated contest.
It could have been much worse for the Merseysiders and they will be confident of turning the narrow deficit around at Anfield next week with a crucial away goal to their name.