Sponichi carried the following list of well-known brothers that played for the same team (listed older brother first):
Shinichi Eto (OF) and Shozo Eto (INF) appeared in 32 games together for the 1969 Chunichi Dragons.
Leron Lee (OF) and Leon Lee (INF) both played for the Lotte Orions between 1978 and 1982. Seems the two hit homers in the same game 28 times.
Hirohisa Matsnuma (P) and Masayuki Matsunuma (P) were teammates on the Seibu Lions between 1979 and 1988. Hirohisa went 112-94 while Masayuki was 69-51.
Kaoru Nimura (OF) and Toru Nimura (INF) were members of the Chunichi Dragons for 5 years beginning in 1988. The two were in the starting line-up for the last time on 10/1/1990. The last time they appeared in the same game was on 10/7/1990.
Satoshi Iriki (P) and Yusaku Iriki (P) became the first brothers to play for the Giants. They appeared in the same game four times between 1999 and 2000. In 2000, the brothers had their names registered as Iriki-ani (older brother) and Iriki-ototo (younger).