Brendan Rodgers' side hammered Arsenal 5-1 at Anfield in the Premier League last weekend, but the London club restored some pride by holding off a late Liverpool fightback to set up a last-eight encounter with Everton.
Alex Oxlade-Chamberlain handed Arsenal an early advantage after 16 minutes, sliding the ball home from inside the area to register a third goal from his last three appearances at the Emirates Stadium.
Oxlade-Chamberlain then turned provider shortly after the interval, pulling a ball back for Lukas Podolski after a smart one-two between himself and Mesut Ozil.
Steven Gerrard's penalty gave Liverpool hope a minute before the hour and the visitors were aggrieved when referee Howard Webb failed to award another spot-kick after Oxlade-Chamberlain appeared to foul Luis Suarez in the area.
Daniel Agger almost grabbed a dramatic equaliser with four minutes left when he headed wide after Lukasz Fabianski came and failed to collect delivery from Gerrard, but Arsenal stood strong to reach the quarter-finals for the first time in three years. Liverpool, meanwhile, are left to focus fully on the Premier League.
Arsenal made seven changes from Wednesday's goalless draw with Manchester United, while Liverpool's notable switch came in goal as Brad Jones replaced Simon Mignolet.
Daniel Sturridge had two early chances for Liverpool, forcing Fabianski into an early save after just a minute before latching onto Suarez's clipped throughball, rounding the goalkeeper and firing into the side netting.
Yaya Sanogo, making a rare start in place of Olivier Giroud, was then involved in a series of Arsenal half-chances before the pressure told as Oxlade-Chamberlain fired home.
The England international was on hand to side-foot home the loose ball after Sanogo's effort was blocked by Gerrard.
Liverpool recovered well and enjoyed a strong spell of possession, but struggled to force Fabianski into any further saves.
A more accurate Podolski cross seven minutes before the break would have offered Sanogo a chance to double Arsenal's lead, while Suarez got a shot away on goal two minutes before the break, only for Fabianski to palm away with a strong right hand.
Podolski doubled Arsenal's lead two minutes after the break when he applied a sweeping finish to Oxlade-Chamberlain's cutback from the byline.
Suarez hit a vicious dipping effort just over the crossbar as he sought to bring Liverpool back into the game while Ozil's save was kept out by Jones soon after.
Gerrard then handed Liverpool a fighting chance from the spot after Suarez was brought down by Podolski in the area before Sturridge almost drew Liverpool level, only for Fabianski to deny him when he looked to have rounded him.
Liverpool felt they should have had another penalty when Suarez appeared to be clattered by Oxlade-Chamberlain in the area, but Webb was unmoved.
Agger then came close to hauling the sides level late on.
Having this week been described as a "specialist in failure" by Chelsea manager Jose Mourinho, who saw his side dumped out of the competition by Manchester City on Saturday, Wenger will now be especially keen to go all the way in the FA Cup after progressing past the fifth round.
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