The final was held on 27 January 2013 and won by Suntory Sungoliath to claim their third Top League title.

Teams ranked 13th and 14th went to the promotion and relegation play-offs against regional challengers to fight to remain in the Top League.

The top 4 teams of 2012–13 were Suntory Sungoliath, Toshiba Brave Lupus, Panasonic Wild Knights, and Kobe Steel Kobelco Steelers.

Coca-Cola West Red Sparks and Kubota Spears won promotion to the 2013–14 Top League via the 2012–13 Top League Challenge Series, while Mitsubishi Sagamihara DynaBoars and Toyota Industries Shuttles progressed to the promotion play-offs.

So Toyota Industries was promoted, Sanix was relegated, and NTT remained in the Top League for the next season.

Awards for the Top League season, including the Best XV, were chosen by a panel of members of the media, coaches and captains.