The decision concludes the only criminal trial to arise from the plant's 2011 tsunami-triggered accident, the world's worst nuclear accident since Chernobyl.
Ichiro Takekuro and Sakae Muto, formerly vice presidents of Tokyo Electric Power Company (TEPCO), had been accused of liability for the deaths of more than 40 hospitalised patients, who had to be evacuated following the nuclear disaster.
Former chairman Tsunehisa Katsumata, who died last year, had also faced the same charges.
The men had faced up to five years in prison if convicted.
But the Tokyo District Court ruled in 2019 that the men could not have predicted the scale of the tsunami that hit the plant.
That verdict was upheld by the Tokyo High Court in 2023, but an appeal was then filed.
The Supreme Court on Wednesday "dismissed the prosecutors' appeals regarding Takekuro and Muto", a top court spokesman told AFP.
"Katsumata's public prosecution was dismissed in November" after his death, he added.
In March 2011, a massive tsunami swamped the Fukushima Daiichi plant on Japan's northeastern coast after an undersea 9.0-magnitude earthquake, the country's strongest in recorded history.
The tsunami left 18,500 people dead or missing.
But no one was recorded as having been directly killed by the nuclear accident, which forced evacuations and left parts of the surrounding area uninhabitable.
Despite the non-guilty criminal court verdict, in a July 2022 verdict in a separate civil case, the same three men and another were ordered to pay a whopping 13.3 trillion yen ($90 billion) for failing to prevent the disaster.
Lawyers have said the enormous compensation sum was believed to be the largest amount ever awarded in a civil lawsuit in Japan -- although they admit that is symbolic, as it is well beyond the defendants' capacity to pay.
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