Djokovic dominated the first set, breaking a sloppy Berdych twice as he exploited the Czech’s inability to land his first serves to great effect.
The second set was a tighter affair as the pair traded breaks, with world number six Berdych even earning a couple of set points as he impressed early in the tie-break.
But Djokovic is a master at digging himself out of holes and he did so in style to win five points in a row, taking the match in one hour and 37 minutes.
Finishing top of his group means the Serb will likely avoid Roger Federer in the semi-finals, with the Swiss defending champion expected to win Group A.
“I was trying not to think about all the (qualification) scenarios, just focused on trying to win the game," Djokovic said. “It’s the first time I’ve won all three group matches so that’s good.
“I know who the crowd wants to win (between Murray and Tsonga) tonight, but I’m just hoping for a good match and that I get enough rest for the semi-finals.”
Berdych, who goes out, paid the price for a terrible service display in the first set.
While he made no double faults, the big-hitting Czech landed under half of his first serves, losing the majority of his points off a slow second serve.
Djokovic, meanwhile, was happy to sit and wait for the Czech to err, which he did to hand the Serb both first-set breaks, first with a backhand to net and then with an errant forehand, both of which came from his usually preferred baseline.
Berdych upped his game in the second set, landing nearly 30 per cent more of his first serves and finding the court with more frequency with his heavy forehands from the baseline.
As a result he was able to break back when Djokovic took his serve, with both men adding some fine drop shots and volleys to their long game.
The tie-break was a thriller too, as Berdych put himself on the brink of forcing a decider after a lovely backhand volley morphed into a drop shot of some beauty, that mini-break extended when he returned a Djokovic lob with interest and aced his next service point.
At 6-3 in the tie-break Berdych would normally be backed against most, but not against Djokovic, who responded with some fantastic deliveries, a crushing return off what could well have been an ace from the Czech, before rounding things off with two more fine serves.
"Yeah, it was quite close set," Berdych said. "I had some chances in the tie-break. If I was able to push him to a third set I may have had some more chances.
"But that's just an 'if'. It didn't happen. It wasn't one of my best matches with (Djokovic) as well."
Djokovic now has a day off before Sunday's semi-final, probably against one of David Ferrer or Juan Martin Del Potro, while Berdych will look forward to Czech Republic's Davis Cup final with Spain later this month.
3-Andy Murray (Britain) beat 7-Jo-Wilfried Tsonga (France) 6-2 7-6(3)
1-Novak Djokovic (Serbia) beat 5-Tomas Berdych (Czech Republic) 6-2 7-6(6)
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