The fine was around £100,000 twice as much as the former all-time record. Gamba Osaka, the opponents in the May 17 match, were fined approximately £50,000.
J-League chairman Kenji Onitake, announcing the penalties said Urawa's management was "gravely responsible for giving an impression to society that football stadiums are dangerous."
Gamba's 3-2 win over Urawa at the Saitama Stadium north of Tokyo sparked what was described as the worst crowd trouble since the league started 15 years ago.
Some 5,000 Urawa supporters blocked 800 Osaka fans from leaving the stadium for three and a half hours.
Urawa apologised to their fans on their website.
A statement said: "We apologise to fans of both teams and all stakeholders. We feel responsible for the fact that we couldn't prevent this trouble and were late in dealing with it. We will review our risk management system and make our stadium more safe and comfortable than before."