Mr Suga received 377 votes in the ruling Liberal Democratic Party election to pick a successor to prime minister Shinzo Abe, who announced last month that he would resign due to health problems.
The other two contenders received a combined 157 votes. Former foreign minister Fumio Kishida took 89 votes, while former defence minister Shigeru Ishiba received 68.
The expected victory in the party vote by Mr Suga, currently the chief cabinet secretary of Mr Abe’s government, all but guarantees his election in a parliamentary vote on Wednesday because of the majority held by the Liberal Democrats’ ruling coalition.
Mr Suga, the son of a farmer in northern Japan’s Akita prefecture, said he had come a long way.
“I will devote all of myself to work for the nation and the people,” he said in his victory speech.
He has said his top priorities are fighting the coronavirus and turning around a Japanese economy battered by the pandemic.
He repeatedly noted his achievements under the Abe-led government when asked about various policies.
Mr Suga had gained the support of party heavyweights early in the campaign upon expectations that he would continue Mr Abe’s policies.
That his victory appears to be a done deal has raised criticism from inside and outside the party that the process is undemocratic and murky.
The closed-door politics also apparently led MPs to support Mr Suga in the hopes of taking favourable party and cabinet posts in his new government.
Mr Abe said, after the vote: “Now I’m handing the baton to new party leader Suga.
“We can count on him.”
Despite his low-key image as Mr Abe’s right-hand man, Mr Suga is known for his iron-fist approach to getting jobs done as a policy coordinator and influencing bureaucrats by using the centralised power of the prime minister’s office.
Mr Suga says that he is a reformist and that he has worked to achieve policies by breaking territorial barriers of bureaucracy.
He has credited himself for achieving a booming foreign tourism industry in Japan, lowering mobile phone bills and bolstering agricultural exports.
Compared to his political skills at home, Mr Suga has hardly travelled overseas, and his diplomatic skills are unknown, though he is largely expected to pursue Mr Abe’s priorities.
In addition to the coronavirus and the economic fallout, Mr Suga stands to inherit several other challenges, including China, which continues its assertive actions in the East China Sea.
He also will have to decide what to do with the Tokyo Olympics, which were pushed back to next summer due to the coronavirus.
And he will have to establish a good relationship with whoever wins the US presidential race in November.