Nishikori, 18th in the world rankings, was a late substitute for world No. 153 Yuichi Sugita and the switch paid off in a 6-4, 7-6 (7-3), 4-6, 6-4 decision over Canadians Frank Dancevic and Daniel Nestor.
Nishikori and Dancevic had each won singles matches Friday and the doubles win Saturday puts the Japanese on the verge of advancing to the Davis Cup quarterfinals in April.
Dancevic and Nishikori square off in the first singles match Sunday with Japan's Go Soeda and Canada's Peter Polansky scheduled for the final match of the series. It will be first-time pairings for both Dancevic-Nishikori and Polansky-Soeda.
Japan jumped out to a one-set lead on the strength of two breaks Saturday. Canada got its first break of the match in the second set but Japan furthered its lead with a win in the tiebreaker.
Dancevic and Nestor extended the match with two third-set breaks but Nishikori and Uchiyama put away the win by saving two break points and getting the only break of the fourth set.
Japan owns a 5-0 Davis Cup series edge over Canada but they haven't played each other since 1939.
The winner of the Japanese-Canada series will go against either the Czech Republic, the two-time defending Davis Cup champions, or the Netherlands in the quarterfinals.