Katsuya Takasu has also promised each player a $30,000 (£23,000) bonus if they win gold, dropping to $20,000 (£15,350) for silver and $10,000 (£7,680) for bronze.
Takasu will see whether his “special donation” has an impact when Nigeria face Germany in the semi-final on Wednesday.
"I hope to see them win gold,” he told the BBC. “They've sacrificed a lot to get to Brazil and reach the semi-finals. Humans with such a strong spirit should be encouraged to perform beyond their own imagination."
And Takasu revealed that this is not the first time he has donated money to a sporting cause.
"I've made previous donations to a Japanese hockey team and other notable causes in the past but this right now with Nigeria is incredibly passionate for me.
"I am deeply determined to motivate this indomitable and strong Nigerian team. I don't want to distract them but to push them further to their target - the gold in Brazil.”
Nigeria’s players boycotted a training session ahead of their quarter-final win over Denmark due to a row over pay.
This news prompted Takasu to step in, with the Nigeria Football Federation (NFF) insisting they will not get carried away.
"I have been in direct contact with Mr Takasu and impressed by his gesture," said NFF vice-president Seyi Akinwunmi.
"But we need not get carried away because the integrity of the country is at stake.
"First we must check about this. Significantly, the team has an important game and we need to focus on that."