In sharp contrast to their efforts in seeing off Aston Villa by the same scoreline in the FA Cup five days earlier, the Blues barely laid a glove on Palace during the first 45 minutes at Selhurst Park.
Chelsea deservedly found themselves behind at the break due to Jefferson Lerma's thunderous strike from distance, but Conor Gallagher brought the visitors level within two minutes of the restart.
Although Chelsea were much improved for the remainder of the contest, it appeared to be heading towards a draw before former Palace loanee Gallagher completed the turnaround in the first minute of added-on time.
Maximum points were sealed later in four minutes of added-on time, Cole Palmer leading a counter-attack and teeing up Enzo Fernandez to confidently convert into the top corner from eight yards to secure Chelsea's 13th successive Premier League win over Palace.
Having ended a two-match losing run in the top flight, Chelsea are back up to 10th position in the standings, just two points adrift of Newcastle United in seventh.
Speaking to BBC Sport after the game, Pochettino admitted that he left disappointed with how Chelsea failed to make any impact in the final third during the first half, yet praised his side for how they responded.
The Argentine said: "We saw two different sides. In the first half we were so flat and I was so disappointed. In the second half much better and I am very pleased with how we finished the game. We deserved the three points.
"The energy wasn't the right energy and the intensity we showed was not great. We dominated but we played so slowly and they way we conceded, we cannot allow to give this type of option to the opponent.
"It is a massive win. That is our challenge to be consistent but this type of fixture will help us build our confidence."
Next up for Chelsea is a trip to play Manchester City at the Etihad Stadium on Saturday evening before they begin preparations for the EFL Cup against Liverpool on February 25.