I think you've confused things a bit:

The Battle of Sekigahara is one of the watershed moments when Nobunaga Oda was able to more or less defeat half of Japan with his arquebus units

Sekigahara was where the Tokugawa forces defeated the forces of Nobunaga's successor, Toyotomi Hideyoshi, and established the Tokugawa Shogunate that would rule Japan for the next 268 years.

it directly led to the Japanese Empire that participated in World War II.

That's a very strange way of putting things. The Japanese Empire that fought in WWII was a product of the Meiji Restoration in 1868, and subsequent developments. It's odd to say Tokugawa's victory at Sekigahara led to it, except perhaps you could say that some of the families of the forces who lost at Sekigahara are the ones who would eventually lead the Meiji Restoration and run the new government.

I would nominate the Battle of Dan-no-ura, which ended the Genpei War in 1185 and led to the end of the Heian period and the establishment of the first Shogunate. The Taira and Minamoto clans had been competing for power at the Imperial court for decades. They fought it out in the Genpei war, which ended with the Minamoto defeating the Taira at Dan-no-ura. Minamoto no Yoritomo then went on to found the Kamakura Shogunate.

As previously mentioned, you seemed to have mixed up some of the events, but to answer what I presume to be your question, the most important battle other than Sekigahara was probably Oda's last actual battle, if you can call it that, at Honnou-ji, where Mitsuhide Akechi led an army against his own lord. At the time, Oda was in a position to take control over all of Japan. The Takeda had fallen earlier in the same year, and the remaining major clans of the Uesugi, Mori, and Hojo were weakened by internal conflict. Of particular note was the fact that Uesugi Kenshin, one of the more skilled generals of the period, had passed away, leaving no clear opponent to Oda's ambitions. In the middle of all this, one of Oda's most trusted retainers marches an army up to the Temple of Honnou-ji and forces Oda to commit seppuku, which is what made Tokugawa's rise even possible.

Admittedly, it's hard to say whether or not this could be considered a true battle, because all Oda had with him were non-combatants like court officials and servants, so it was a little one-sided. The Wikipedia page actually refers to it as the Honnou-ji incident, rather than as a battle, but in my opinion, this was the most significant battle of the Sengoku period, possibly even more so than Sekigahara, as it's hard to say if Sekigahara would have happened without Honnou-ji.

I believe you are amalgamating the battle of Nagashino with the Battle of Sekigahara.

As for important battles, I'd argue Okehazama. Okehazama, unlike many of the other battles mentioned here, wasn't the "culmianting" or "final battle" of a particular campaign, per se: rather, Oda's inferior force was able to break through Imagawa Yoshimoto's lines, which allowed them to kill him and break Imagawa's power-subsequently opening up the area for Oda to dominate and leaving him with no real major threats aside from enemy coalitions.

The most important moment in the history(not only medieval) of Japan, is the death of one of the authorities rather than one of the battle.
Ashikaga Yoshimitsu, is the only man who tried to destroy the emperor system.