Receiving the accolade for the second time, Hara led Japan to its second consecutive World Baseball Classic title and Yomiuri to its third consecutive Central League pennant and first Japan Series crown in seven years.
Hara, who also won the Shoriki award as the Giants manager when they took the Japan Series title in 2002, was unanimously chosen by the five-man selection committee.
"I am very grateful to receive this award just by being the manager for the WBC team and for the Giants. This was a long year. I would like to think that some of the hard work, struggles and efforts paid off," Hara said.
"I still have a lot to learn in terms of being a manager and as a person. I want to use this as a stepping stone to continue to reach greater heights."
Former Softbank Hawks manager Sadaharu Oh acted as chairman of the committee in the absence of former Giants manager Tetsuharu Kawakami, who decided to sit out due to his advanced age.
"If you were to hold an election throughout Japan now I'm sure the same thing would happen. That's how little divergence of opinion there was," said Oh.
New York Yankees designated hitter Hideki Matsui, who won MVP honors in the World Series, had also been mentioned by the committee but he was left out of selection since the Shoriki award is only reserved for the best in Japanese baseball.
Aside from Oh, Shigeru Sugishita, Futoshi Nakanishi, Keiji Osawa and Masao Taguchi also sat on the selection committee.
The late Shoriki, once president of the Yomiuri Shimbun, was instrumental in the establishment of professional baseball in Japan.