And in a dramatic finish Julius Aghahowa glanced a stoppage-time header just wide when he really should have scored.
Liverpool's record buy Fernando Torres had had chances galore in the first half, but the lethal touch he showed when he hit a Carling Cup hat-trick against Reading deserted him and it was goalless at the break.
But there was controversy when Wigan twice had strong penalty appeals turned down.
A Michael Brown shot struck Steven Gerrard on the arm and in the other incident Paul Scharner was flagged offside as Aghahowa appeared to be brought down in the box by Jame Carragher.
The Reds had produced the first threat of the game when skipper Gerrard forced his former team-mate Chris Kirkland into action after just 66 seconds.
He beat the wall with a well struck free-kick but Kirkland got down well to hold it safely.
Torres had his first sniff when strike partner Dirk Kuyt played him in but the shot lacked power and Emmerson Boyce blocked it.
Jermaine Pennant had one effort deflected off course and three times Torres found himself in good positions but failed to cash in.
A mistake by Jason Koumas gifted him a real chance but Kirkland used his legs to block and the rebound went wide.
For Wigan Marcus Bent tried his luck from long range and a speculative strike from Josip Skoko failed to trouble Jose Reina.
Torres looked in vain for a penalty when he went down under a challenge but the replay revealed no contact.
But the Wigan claims - rejected by the ref - looked more convincing.
The Latics did have the ball in the Liverpool net when Bent hammered in Skoko's cross but he was ruled offside.
Koumas had Reina at full stretch and Kirkland earned his money keeping one out from Kuyt as the game opened up.
There was more drama as Scharner chased a long ball into the box, but he was beaten by the bounce after getting a slight touch, and it went wide.
Gerrard rattled one just past the post as the Reds turned the screw and the reward came when Benayoun raced on to Pennant's pass, turned Titus Bramble and Kirkland was finally beaten.
Wigan tried desperately to salvage a point with Ryan Taylor going close and Aghahowa missing with that late header.