Nishikori built a 6-2, 1-0 lead over Frank Dancevic when Dancevic pulled a stomach muscle and was unable to continue, ceding the match to Nishikori and putting Japan ahead 3-1 in the best-of-five series.
Go Soeda added on a 6-1, 6-4 win over Peter Polansky to make the final score 4-1 Japan.
The Japanese will go against either two-time defending champion Czech Republic or the Netherlands in the April 4-6 Davis Cup quarterfinals.
Nishikori opened the series Friday with a 6-4, 6-4, 6-4 win over Polansky but Dancevic topped Soeda 6-4, 7-6 (7-2), 6-1 in the second singles match, leaving the team tied 101 after the first day. Nishikori teamed with Yasutaka Uchiyama for a 6-3, 7-6 (7-3), 4-6, 6-4 win over Dancevic and Daniel Nestor for a doubles win Saturday.
Nishikori didn't face a break point against Dancevic Sunday and had a pair of breaks in winning the first set. Dancevic said the stomach injury occurred in the second set while serving. Nishikori won that game and Dancevic said he was unable to continue.
Soeda's victory came as he had a pair of breaks in each set and won more than half the points off Polansky's serve.