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The Serb, 27, won 6-2 6-2 to extend his unbeaten run indoors to 30 matches stretching back to 2012.
He tops Group A in London with three wins and will play Kei Nishikori in the semi-finals on Saturday.
Stan Wawrinka will play Roger Federer in the second semi as he won the three games required against Marin Cilic.
Wawrinka, the Australian Open champion, took only 13 minutes to move 3-1 ahead and so ensure he could not be overtaken by Cilic in any of the qualification scenarios.
The Swiss number two went on to win 6-3 4-6 6-3 and return to the last four after his debut appearance 12 months ago.
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Czech player Berdych, 29, suffered a 17th defeat in 19 matches against Djokovic but made more of a mark than in their last meeting, when he trailed 6-0 5-0 in Beijing last month before grabbing two games.
A similar drubbing appeared on the cards when the Serb raced into a 4-0 lead with two breaks of serve.
After a week of one-sided matches at the O2 Arena there was relief all around when Berdych recovered from 15-30 to get on the scoreboard in game five, but it was hardly a signal of intent.
Djokovic continued to dominate, rolling through the first set in 31 minutes and making it five games in a row as he moved 4-0 clear in the second.
Berdych slowed the two-time champion's progress sufficiently to take him past the hour mark, but Djokovic sealed victory after 69 minutes, and with it the end-of-season number one ranking for the third time in his career.
"Definitely one of the best," Djokovic said of his performance. "Obviously I hoped I could continue the way I played in the first two matches.
"It's been a long year, a long season, it's an incredible achievement and I want to thank my team and my family and all the people who supported me.
"I'm aware that being number one in the world is the biggest challenge a tennis player can have. It's an incredible feeling and I'm very happy."
Meanwhile, Wawrinka was left to look ahead to Saturday's second semi-final where he will face compatriot Federer.
"I hope I can get a little bit of support because I know people love him here. It's going to be tough for me, but I need to trust myself and go for it," said Wawrinka.
"It was a tough match tonight, it's never easy to play against Marin, he's been having an amazing year. It was not easy, trying to be aggressive. I was trying to serve and volley."
Novak Djokovic brushed aside Tomas Berdych to reach the last four at the ATP World Tour Finals and secure the year-end number one ranking.