The Serb came into the contest seeking to win one set to secure his spot in the final four.
He did so in dominant fashion, brushing his Czech opponent aside 6-3 to take the opener.
Having been in cruise control for the first set, Djokovic then came up against greater resistance in the second, as Berdych made a fist of it.
But the Serb eventually triumphed on a tie break to advance as the winner of Group A and will be the man everyone wants to avoid in Sunday's semi-finals.
He said: “I didn’t want to think about scenarios or calculations, I’ll leave that to other people. I try to do my job and win on the court, I played a really good match but I thought he served better towards the end.”