Days after announcing he was leaving in the summer after a 17-year professional career at the club, Liverpool captain Gerrard put the Reds ahead after 12 minutes with a fine header.
But Adebayo Akinfenwa equalised nine minutes before half-time after the ball dropped to the feet of the giant striker three yards from goal.
League Two Wimbledon had a flurry of chances either side of half-time, but it was Gerrard again who gave Liverpool the lead, firing home a trademark free-kick from the edge of the box.
Reds boss Brendan Rodgers fielded a fairly strong side, starting the likes of Gerrard, Simon Mignolet, Jordan Henderson and Philippe Coutinho, and both sides knew they would be meeting Bolton Wanderers in a home tie in the fourth round before kick-off.
The game lived up to the pre-match hype having evoked memories of Wimbledon’s 1-0 FA Cup final win over Liverpool in 1988.
And Liverpool’s one clear-cut chance in the first half resulted in a goal, and it was the skipper who netted.
Javi Manquillo’s right-wing cross was headed home by Gerrard from 12 yards out after a move involving Lambert, but the hosts reduced the Premier League side’s chances for the rest of the opening 45 minutes.
Wimbledon went close to an equaliser midway through the first half after a melee in the area resulted in Sean Rigg’s volleyed effort being tipped over the bar by Mignolet.
Minutes later the ball fell to top scorer Matt Tubbs inside the area after Manquillo let the ball drop, but the striker knocked the ball just wide with just Mignolet to beat from a slight angle.
The League Two side levelled on 36 minutes through Akinfenwa, sliding home from three yards after Barry Fuller had hit the bar from a George Francomb corner.
Question marks were asked again of Belgian goalkeeper Mignolet, who failed in his attempt to clear the original ball into the box under pressure from Wimbledon players.
Adam Barrett saw a header cleared off the line by Gerrard in the second half, before Coutinho shot wide from an angle when passing to his captain looked the better option.
But when Coutinho was brought down on the edge of the area by Fuller, Gerrard stepped up for his ninth goal of the season, curling a perfect free-kick past James Shea.
A minute after the goal, the hosts went down the other end through Dannie Bulman, but his header went just over Mignolet’s goal.
The second half saw a flurry of chances fall to Liverpool; first Lambert’s side-footed effort was saved by the leg of Shea, before Coutinho brought another save from the Wimbledon stopper when he should have scored.
With six minutes remaining, Adebayo Azeez saw a powerful effort blocked well by defender Martin Skrtel in the Liverpool box, before Liverpool broke from the resulting corner, only for Lazar Markovic to see his effort saved fantastically by Shea again.
Azeez again looked to get on the end of a knock down in stoppage time from six yards out, only for Mignolet to save with his feet, before Gerrard’s effort at the far post went through Shea’s legs but couldn’t beat Jake Goodman on the line.