Suga won 377 of the 535 available votes on Monday, the LDP announced.
The LDP, which has ruled mostly uninterrupted since 1955, is now set to use its parliamentary majority to replace the outgoing prime minister Shinzo Abe with Suga in a separate vote on Wednesday.
"We cannot have any void in policy," Suga said after the vote. "It is my mission to carry forward what has been done under Prime Minister Abe."
"I want to create a government that people can trust. I will push ahead with deregulation and put an end to ministry sectionalism, endemic vested interests and the practice of blindly following past precedents," Suga added. "I will create a working cabinet."
Abe, who has served since 2012, announced on Aug. 28 that he would step down due to poor health after a relapse of an intestinal disease called ulcerative colitis, just days after he became the longest-serving prime minister in the country's history in terms of consecutive days in office.