Murray replaced him as number one last week, and the Scot plays Marin Cilic in his opening match in the John McEnroe Group on Monday.
He reaches the semi-finals with three round-robin wins and Djokovic is runner-up with one round-robin win.
Thiem had not beaten Djokovic in their previous three meetings but normal service was resumed in a second set of real contrast.
Djokovic himself held his first set a few points later up 9-8. He started making more errors, which I used.
That was Nishikori's first semi-final appearance at a major since his run to his only Grand Slam final in NY in 2014 and the 26-year-old hopes it is a sign he is finally ready to fulfil the potential that saw him labelled as a potential champion when he first burst onto the ATP Tour.
The action kicks off on Sunday afternoon, with Novak Djokovic beginning his campaign to get back to the top of the rankings when he faces Dominic Thiem at 2pm. "All in all it was an unbelievable experience to play in front of this great crowd", Thiem said after the loss. But it appeared to help fire him up for a comeback and he immediately broke serve in the first game of the second set.
He explained: "Winning the French Open this year has brought a lot of joy to me but on the other hand has taken away a lot from me, as well". I'm going to be able to prepare a good plan for the match.
Should Andy Murray end the season as the world number one tennis player - the feel inside his team is that it would be deserved, says Jamie Delgado.
But Djokovic couldn't find a breakthrough and the set went to a tie-break.
The Scottish star became the world's best player last week and must match or better Novak Djokovic's performance in London to stay top of the pile.
But the Serb, who reigned 122 weeks at the top of the rankings, put a decade of elite tennis to best use as he stormed back to take the second set in 20 minutes. I don't feel any different this week than I did the week before, maybe when you step on the court you have a little more confidence. "I'm playing Stan in the first match and he's having a great season", Nishikori told reporters in London. I learned a lot from those matches. "It's faster than it has been in the past so that changes the way you play the matches a little bit", Murray, 29, said.
"It's incredible what he's doing right now, not only his level, but his consistency and how he keeps winning", the Swiss star said.
"It took a bit of time to get back on track but all in all it was a very good year".