South Korean international Ji Soyun scored the game-winning goal to clinch the league with four games remaining, putting Kobe in contention for a domestic treble
After a scoreless first half, Chiaki Minamiyama's opener in the 64th minute was canceled out 10 minutes later by Vegalta striker Hitomi Ono. It took less than five minutes for the game-winner to arrive courtesy of midfielder Ji Soyun in the 78th minute.
With four games remaining in the season, the victory gave INAC an unassailable 13-point lead over second-place NTV Beleza.
"I'm glad we were able to win the championship," Kobe veteran Homare Sawa said after the match. "A lot of games didn't go as we expected and there were struggles, but we played together and earned this result."
Team-mate Nahomi Kawasumi agreed: "All I can say is how happy I am. It was important that we grew so much as a team."
The championship also completes a historic third straight double for INAC, who will become the first Japanese women's club to sign the entire squad to professional contracts beginning in 2014.
In addition to competing in the 2013 International Women's Club Championship in November, INAC can potentially claim an unprecedented domestic treble by winning the Empress's Cup, which will be contested by 36 clubs in November and December.