Murray survived the longest three-set match in ATP Finals history when he prevailed against Nishikori 6-7 (9), 6-4, 6-4 on Wednesday (Nov 16).
They needed 3 hours, 20 minutes, to separate themselves. The first set alone took 85 minutes.
Murray, 2-0 in his group, can clinch a semifinal berth for the first time in four years with a win over US Open champion Stan Wawrinka on Friday.
Wawrinka eliminated Marin Cilic from contention 7-6 (3), 7-6 (3) in an almost two-hour-long late match.
Losing to No. 5-ranked Nishikori would have hurt Murray's chances of holding off Novak Djokovic to keep the No. 1 ranking. Murray relieved Djokovic of the top ranking last week, and Murray believed it would be a fitting end to the year to play the Serb for the ranking and ATP Finals title on Sunday in the final.
"For the tournament and stuff, for everyone interested in tennis, that would probably be the perfect way to finish the year," Murray said.
"For me and, I'm sure, for Novak, both of our goals would be to try to win the event. It doesn't change for us as players."
Murray admitted he abused himself on court more than usual while trying to figure out how to overcome Nishikori.
"He could have won in two sets, for sure," Murray said. "He moves the ball around extremely well, better than anyone maybe. It was physically tough. I wasn't able to dictate many of the points, it felt. More so in the third set I was able to. But not in the first couple of sets. I was having to run, fight, get as many balls back as I could.
"I feel OK right now. It's normally the next day when you feel stiff and sore, but there's hopefully three days left in the season, and I'll give my best to get through as many matches as I can."
For all of Murray's achievements this year, this was the first time he played a top-five opponent since June, when he lost to Djokovic in the French Open final. Nishikori was one of only three players to beat him in the intervening five months, edging a five-setter in the US Open quarterfinals.
They also went five sets and almost five hours in the Davis Cup in March. Nishikori extended their first set on Wednesday when he saved a set point at 6-5 down, but he needed four set points to take the opener on a wide forehand by Murray.
Murray immediately broke to start the second. Nishikori tied it at 4-4. But Murray broke straight back, and had to save two set points to force a decider.
Murray has played more matches than ever this season and he looked drained, but Nishikori's decision-making was clouded by fatigue, and he lost his serve in the third game.
When a double fault made it 4-1 to Murray, the Scot finally had some breathing space and the end in sight.
Nishikori showed commendable resolve to retrieve one break, but Murray served out at the second time of asking for his 21st successive win. Murray has a chance to match his best streak of 22, from June to August, when he plays Wawrinka on Friday to end group action.
Wawrinka saved one set point in the first set, and dominated the tiebreaker. Cilic broke to open the second, but Wawrinka got him back and served too good in the tiebreaker again for his 11th win in 13 matchups with Cilic.