The rules nobody tells you
Japan is a society built on consideration for others. The stadium is no exception. These aren't written on the ticket, but every Japanese fan follows them.
Don't wear the wrong team's gear in the wrong section
This is the big one. Home team outfield is for home fans. Visitor outfield is for away fans. Wearing a Tigers jersey in the Giants outfield section will get you confronted. Infield seats are neutral territory — wear whatever you want.
Clean up your own trash
After the game, pick up everything around your seat. Beer cups, food wrappers, everything. Japanese fans do this automatically. The stadium is nearly spotless after 46,000 people leave. Leave your area cleaner than you found it.
No umbrellas
Even if it's pouring rain at an outdoor stadium, umbrellas block the view for people behind you. Bring a rain poncho instead. This rule is enforced.
Move during breaks, not during play
Walk to the bathroom or food stall between innings (baseball) or at halftime (football). Walking in front of seated fans during live play is rude. Wait for a natural break.
Don't throw things
No throwing anything onto the field. No throwing beer cups. No throwing anything at all. What seems like harmless fun elsewhere is a serious offense in Japan.
Foul ball awareness
In the infield, foul balls are a real danger. Pay attention when the game is live. If you catch a foul ball, keep it — it's yours. Unlike some countries, there's no expectation to give it to a child.
The one exception to quiet
The outfield cheering section is loud by design. Singing, chanting, standing — all expected. If you sit there, participate or at least don't complain about the noise. If you want a quiet experience, sit in the infield.