The Liverpool captain - who announced his plans to leave Anfield at the end of the season on Friday - struck in both halves at Kingsmeadow to dash League Two Wimbledon's hopes of repeating their famous victory in the 1988 final.
Gerrard perfectly timed a run into the penalty area to head home the opening goal after 12 minutes, but Liverpool were pegged back by Adebayo Akinfenwa's close-range leveller before the interval.
Wimbledon had further chances to add to that goal, but it was Gerrard who was the match-winner with a superbly placed free-kick after 62 minutes.
Brendan Rodgers' men were able to keep their opponents at arm's length in the closing minutes to set up a tie with Bolton Wanderers in the fourth round.
Akinfenwa returned as one of two changes for the hosts, but it was his strike partner Matt Tubbs who threatened early.
The 30-year-old latched onto an eighth-minute flick from Akinfenwa, but he dragged his shot wide of Simon Mignolet's goal.
Neal Ardley's men were made to pay four minutes later as Gerrard marked his first Liverpool game since declaring his intention to leave the club by breaking the deadlock.
He got on the end of a pinpoint delivery from Javier Manquillo – one of four Liverpool alterations – and neatly placed his header beyond James Shea.
Having soaked up plenty of pressure, Wimbledon slowly battled back and just before the half hour saw Sean Rigg denied by a superb reflex save from Mignolet.
However, the goalkeeper was all at sea in the 37th minute as he failed to claim a George Francomb corner, and Akinfenwa was on hand to fire Wimbledon level.
The fourth-tier side went close to taking the lead two minutes after the break, but Adam Barrett's looping header from a right-wing corner was cleared off the line by Gerrard.
Wimbledon were lucky to survive a 56th-minute appeal for a penalty when Barry Fuller handled inside the area, with referee Jon Moss waving away the Liverpool appeals.
The full-back was not so fortunate five minutes later, though, as he felled Philippe Coutinho with a reckless lunge on the edge of the box.
He was immediately punished by Gerrard who curled the free-kick over the Wimbledon wall and out of the reach of Shea.
Rickie Lambert – who had been anonymous in the opening hour – almost extended their lead even further in the 69th minute, only to fluff his lines.
The striker was released by Gerrard inside the penalty area, but his low shot was kept out by the legs of Shea.
Gerrard had an opportunity to wrap up a hat-trick with nine minutes remaining, but Shea was alert to deny him as the plucky hosts were narrowly beaten.
