Pochettino made seven changes and rested a host of players against the local rivals, who are 63 places below them in the football pyramid in League Two.
James Tilley opened the scoring after Robert Sanchez gave away an early penalty before Noni Madueke scored and won a penalty of his own just before half-time.
Chelsea needed £260million worth of players to secure victory in the second half with Enzo Fernandez, Moises Caicedo, Malo Gusto and Nicolas Jackson all coming on.
Enzo saves Chelsea from a poor second-string display
Enzo Fernandez and, to a lesser extent, Moises Caicedo were needed to save Chelsea in the second half.
The Argentine changed the game upon his introduction in the 65th minute immediately producing a stunning shot with Wimbledon’s deep backline struggling to close him down.
He then equalised after capitalising on a mistake by goalkeeper Alex Bass, curling in a finish from 25 yards as the shot-stopper was stranded outside his net.
Caicedo was brought on to shut up shop late on but a host of younger players struggled. Diego Moreira was taken off at half-time, Mason Burstow made little impact on his first start and Lesley Ugochukwu faded after a positive start.
An out-of-position Bashir Humphreys struggled at right-back, leaving the question of how can Chelsea be short of depth if they have spent over £400m?
Colwill injury concern
Levi Colwill appeared to pick up a muscle injury midway through the second half during one of Wimbledon’s many dangerous attacks.
It leaves him doubtful to face Nottingham Forest on Saturday and, unfortunately, for a potential England call-up, with Gareth Southgate’s squad announcement coming on Thursday afternoon.
Colwill could really have done with using the international break to audition for Euro 2024.
Maatsen is a wide player
Ian Maatsen played as a no10 as he had done in pre-season, but struggled against a well-organised opponent.
The 21-year-old has spent most of his career as a left-back with the occasional appearance in a defensive midfield position but hasn’t proved himself an an attacker in Pochettino’s competitive matches.
He struggles even more when asked to play centrally, despite his obvious technical gifts. He created little from central areas and wasted scoring opportunities.
He did, however, create the winner by chasing a lost cause which allowed Enzo to kill off the lower-league side.