Nishikori, who has lost eight ATP finals since his last win in Memphis in 2016, is still in with an outside chance of joining Anderson and company in London.
His qualification means there are two places still up for grabs ahead of this week's Paris Masters, with Croatian Marin Cilic, Austrian Dominic Thiem, Nishikori and American John Isner still in the race.
"He was a tough opponent", Nishikori said after remaining undefeated against Kukushkin in eight career matches.
After the win, Anderson improved his head-to-head record against Nishikori to 4-3, earning his second victory in a row this year against the Japanese player, following his NY semifinal triumph.
Anderson, with only four ATP World Tour 250 championships to his name, would qualify for the ATP Finals by capturing the Vienna title.
After pushing for the break in the decider, Anderson finally converted on his sixth break point opportunity of the set to seal the win in the final game.
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Nishikori leads the field with 60% of second-serve return points and 38% of return games won in the tournament before the match, and the semifinal confirmed the trend as Kukushkin won just 57% of second serve points.
The 32-year-old is the first South African to reach the ATP Finals in 23 years and follows in the footsteps of compatriot Wayne Ferreira who achieved the feat in 1995.
Anderson has a shot at a fifth career title and second of the year after winning in NY in February.
BASEL, Switzerland (AP) - Roger Federer advanced to the 14th Swiss Indoors final of his career by beating seventh-seeded Daniil Medvedev 6-1, 6-4 on Saturday. The next break point did not come until the 10th game.
The Japanese star triumphed 6-4 6-3 to improve his record against the Kazakh to 8-0.