Abe, who resigned earlier on Wednesday along with his cabinet, had on August 28 announced his exit, ending his record run in office with a year left in his mandate.
He was forced out by a recurrence of ulcerative colitis, a bowel disease that has long plagued him.
Suga, 71, won an easy victory, taking 314 votes of 462 valid ballots cast in the lower house of parliament, where his ruling Liberal Democratic Party (LDP) holds a commanding majority.
He bowed deeply as lawmakers applauded following the announcement, but made no immediate comment.
Lower house speaker Tadamori Oshima, announcing the result after the votes were counted, said;
According to the results, our house has decided to name Yoshihide Suga prime minister.
The new Prime Minister is expected to announce his cabinet later Wednesday, with local media reporting he will retain a number of ministers from Abe’s last government.
Suga, who on Monday was elected leader of the LDP, is viewed as a continuity candidate and has said his run was inspired by a desire to pursue Abe’s policies.
He has spent decades in politics — most recently as chief cabinet secretary, where he was known for pushing government policies through a sometimes intractable bureaucracy.
Suga has also been the face of the government, doggedly defending its policies as spokesman, including in sometimes testy exchanges with journalists.
He has said kickstarting the economy will be a top priority, along with containing the virus — essential if the postponed Tokyo 2020 Olympics are to open as planned in July 2021.
On the diplomatic front, Suga is a relative novice, with little foreign policy experience.
Experts say he is likely to tread the path charted by Abe, prioritising the key relationship with the United States, whoever is president after the country’s election in November.
Relations with China may prove trickier with a global hardening of opinion against Beijing after the coronavirus and unrest in Hong Kong.
Abe will stay on as a lawmaker, with some mooting the possibility he could undertake diplomatic missions.
On Wednesday morning as he prepared to resign, Abe said he had given “all my strength” and is ending his tenure “with a sense of pride”.