Anderson has a shot at a fifth career title and second of the year after winning in NY in February.
Nishikori's title drought on the ATP World Tour spans eight losses in finals, more than two years and 48 tournament appearances.
Appearing in his fifth tour-level final of the season, Anderson captured his second trophy of the year after one hour and 55 minutes. But reaching Sunday's final, his third of the season, boosted the fifth-seeded Japanese's chances of also advancing to the ATP finals.
Nishikori still leads Anderson 4-3 in their head-to-head statistics, though he lost both of their matches this year.
Anderson was runner-up to Novak Djokovic at Wimbledon this year but the win in Vienna represented the biggest title of his career.
Nishikori held serve throughout against Kukushkin, who came through qualifying.
A tight second set went to a tiebreak with Anderson landing his 13th ace of the match to win his landmark title.
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.
On Saturday, he missed three break points in the first set before finally breaking in the 10th game with an aggressive forehand victor.
He's the first South African to reach the Finals series since Wayne Ferreira in 1995.
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 German made in six wins from seven matches with a 7-5 6-3 defeat of Roberto Bautista Agut, and will now face Marius Copil after the Romanian defeated Taylor Fritz 7-6 (8-6) 7-5.