Vasek Pospisil, ranked 62nd in the world, fired 14 aces in his 7-5, 6-3, 6-4 victory over Go Soeda, who was drafted for singles duty in place of Tatsuma Ito, who fell to Milos Raonic in straight sets.
Nishikori's teammate Go Soeda held his nerve to beat Alejandro Falla 4-6 6-4 6-3 6-3, triggering wild celebrations in Tokyo.
The 2008 runner-up was made to work hard for his 6-3, 7-6 (7/1), 6-3 win over 73rd-ranked Soeda in 2hr 3min in hot temperatures on Margaret Court Arena.
Japanese tennis stars Kei Nishikori and Go Soeda are ATP Tour opponents one week, and Olympic teammates the next.
Kei Nishikori became the first Japanese man to reach the Wimbledon third round for 17 years as the 19th seed crushed France's Florent Serra 6-3, 7-5, 6-2 on Thursday.
Former champion Tommy Haas withdrew with a right knee injury on Monday during qualifying in the U.S. Men's Clay Court Championships.
Japanese qualifier Go Soeda upset defending champion Stanislas Wawrinka of Switzerland 6-4, 6-4 in the Chennai Open quarterfinals on Friday.