Murray was pushed to his limits by Nishikori in the longest Tour Finals match played in the event's seven years.
Murray was pushed to his limits by Nishikori in the longest Tour Finals match played in the event's seven years at London's O2 Arena.
The 29-year-old finally subdued the Japanese star in three hours and 20 minutes, but he was made to wait for confirmation of a last-four berth after Stan Wawrinka beat Marin Cilic 7-6 (7/3), 7-6 (7/3) in the evening match.
Given the complex nature of the Tour Finals rule book, Murray now takes on US Open champion Wawrinka on Friday with his fate still to be decided, while Nishikori also has a chance of reaching the semi-finals when he faces Cilic.
If Cilic beats Nishikori on Friday, then both Murray and Wawrinka can go through.
"I just fought really hard. Kei was making me run but I eventually got over the line," Murray said.
"These are the sort of matches you work so hard for. I feel OK right now, but it's the following day when you feel it often.
"Hopefully there will be another three days to this season and I'll do my best to get through them."
Murray's gritty recovery took his winning streak to 21 matches, just one short of his career best run of 22 successive victories earlier this year.
It is the first time Murray has started the Tour Finals with two consecutive group stage wins since his tournament debut in Shanghai in 2008.
Murray's refusal to be outlasted by the obdurate Nishikori keeps him on course to retain top spot in the ATP rankings at the end of the year.
Novak Djokovic's win over Milos Raonic on Tuesday had given the Serb a 70-point lead over Murray in the unofficial 'as-it-stands' rankings but, with each victory at the Tour Finals worth 200 points, the Scot moved back above his old rival by beating Nishikori.
To guarantee finishing 2016 in pole position, Murray must win the Tour Finals for the first time, with anything less giving Djokovic the chance to overhaul him.
Nishikori is still in with a chance of making the semi-finals despite the loss and he said: "It was close. Andy's a tough player.
"I'm definitely disappointed. But there's much to play for, so I try to be ready for that.
"I played really consistent, with good energy. I'm sure Andy's going to qualify from the group and I'll try to aim for the second spot."
Murray was involved in the previous longest Tour Finals match, a 2010 semi-final loss to Rafael Nadal that took three hours and 11 minutes, and this time his overtime wasn't in vain.
While saving break points in the third and fifth games of the first set, Murray was pushed so hard that his wedding ring, which he keeps tied to his shoe, fell off.
In a thrilling tie-break, Murray came from 3-6 down and saved four set points but crucially he was unable to take two set points of his own and Nishikori finally sealed it when the Scot missed a wild forehand.
It had taken 85 minutes to settle a gruelling first set, yet Murray's energy levels remained high and he started the second set with an immediate break.
Nishikori responded by levelling at four-all, only for Murray to break again and close out the set.
Even after more than two and half hours on court, Murray's renowned commitment to his fitness ensured he was still going strong in the final set and he broke in the third game.
Murray broke again, yet Nishikori didn't go quietly and he got one break back before the Scot at last aced one of his most demanding tests this year.