The Spaniard, who started strong and seemed headed to his third straight-set win before losing his way, still advanced to Saturday's semifinals and will next take on Switzerland's Roger Federer, a five-time winner of this event.
Ferrer, who could have avoided a Saturday match-up with the Swiss great by defeating Berdych, came out determined in the early going at London's O2 arena, snagging a break of serve in the eighth game to take the first set.
The second set was an up-and-down affair, with Ferrer twice going up a break of serve only to play nervously and cautiously and allowing Berdych to take the initiative in the rallies and level the set both times.
Then in the 12th game of the second set, the big-hitting Czech struck again, breaking Ferrer's serve a third time when the Spaniard sent a ball over the baseline.
By winning the set, Berdych assured himself a spot in Saturday's semifinals but both players still wanted the win to top the group and set up a semifinal match against the runner-up in Group B, France's Jo-Wilfried Tsonga.
In the decider, Berdych rode his momentum to a big lead over his discouraged opponent, who lost the consistency on his backhand and the rhythm on his serve and could only manage a single game.
"I think I was playing good the first set, and (then in) the middle of the second maybe at 4-3, 40/15, I didn't serve really well," Ferrer said in the post-match press conference.
"I served very badly and I played my shots very short. In the third set, he was playing with more confidence. When it's not working, my serve, it's very difficult to beat the top players."
Ferrer also advanced to the semifinals of this elite, indoor hard-court event in 2007, when he made it all the way to the final before losing to Federer in straight sets.
The Barclays ATP World Tour Finals, a year-end event limited to the top eight players in the ATP rankings, is regarded as the fifth-most prestigious tournament on the men's tennis calendar after the four Grand Slams.