After Federer's 7-5, 4-6, 6-4 win earlier in the day, world number one Djokovic knew he would advance to the last four if he could secure one set against Berdych in his concluding group match at London's O2 Arena.
The Serb, a winner of three Grand Slam titles this year, wasted little time achieving that goal as he took the first set to ensure he would finish second in the group behind Federer and eventually eased to victory in 89 minutes.
Federer, who has won the Tour Finals a record six times, will face either Murray or Wawrinka, who clash on Friday, in the semi-finals.
Losing to Federer in straight sets would never be an easy result to stomach for the ultra-competitive Serb, but it was especially painful since it ruined his three remarkable winning streaks.
But, with his tournament survival on the line, Djokovic could take comfort from winning 20 of his previous 22 meetings with Berdych, including their last seven matches and all four of their Tour Finals encounters.
- Lucky break -
===============
He fired off a string of winners and took seven of the first eight points to break in the second game of the first set.
Berdych broke straight back, but Djokovic got a lucky break that helped him seal the set when the former Wimbledon runner-up failed to challenge on a call that would have gone in his favour.
Berdych had already lost his first two group matches and when Djokovic broke in the opening game of the second set he could easily have crumbled.
But the 30-year-old kept plugging away with his booming forehand and induced enough Djokovic errors to break back three games later.
Faced with that sudden barrage, Djokovic responded in typically combative fashion and gradually wore down Berdych, breaking for a 6-5 lead before serving out the win.
Federer had already clinched a record 13th Tour Finals semi-final place after ending Djokovic's three-month unbeaten run.
"It was a really important one for me, to move on (to the semi-finals) with a good feeling," Federer said.
"There's points on the line and prestige, wanting to beat Kei, winning at the O2. I want to do well here."
Nishikori added: "Each set I didn't start well. Every time he broke first and I was on the defensive all the time. That was my big mistake.
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