Vice President Kamala Harris and the prime ministers of Australia, South Korea and India were among the dignitaries from 50 countries to attend the event in the Japanese capital.
Abe's widow, Akie Abe, carried his ashes from their home to the Nippon Budokan Arena, where the funeral was held.
Tables set up to accept flower tributes from the public near the funeral site drew a large crowd, with wait times reaching up to two hours in the morning before the funeral, according to the country’s public broadcaster NHK.
But the state funeral for Japan’s longest-serving prime minister, who was shot and killed while campaigning in Nara on July 8, takes place in a country deeply divided over the former leader’s legacy.
Tokyo remained under maximum security, with around 20,000 officers patrolling the city, as two separate crowds gathered in the city: one to pay tributes to the former leader and another to protest his state funeral.
Backlash against Abe’s Liberal Democratic Party has grown since his death, with many taking issue with his purported ties with the Family Federation for World Peace and Unification, widely known as the Unification Church, which have come to light in the wake of the assassination.
The church has denied that Abe was an adviser or a member of its congregation, but he made a speech at the church last September, according to information on the church's website.
The church, which conducts mass weddings and is notorious for its aggressive fundraising from its congregation, is considered by its critics to be a cult.
In addition, the lavish funeral set to cost almost $12 million in taxpayer money comes at a time of economic uncertainty for Japan.
Some opposition politicians, including the leadership of the opposition Constitutional Democratic Party, boycotted the funeral.
“It is only natural that we offer our condolences to the deceased. In that sense, I would like to once again offer my sincere condolences to former Prime Minister Abe, who was killed by a bullet,” its leader, Kenta Izumi, said Tuesday.
“We are opposed to the state funeral because of the lack of precedence and the fact that the decision was made without the involvement of the Diet, which is very problematic,” he continued, referring to the Japanese parliament.
State funerals are very rare in Japan, with the last one being held in 1967. The decision on whether to hold a state funeral is usually subject to parliamentary deliberation, which was not the case for Abe's service.
Around 800 people protested the state funeral at a major train station Monday evening, according to the broadcaster NTV. One man in his 70s set himself on fire in apparent protest last week outside the prime minister's residence, according to several local media reports.
Public sentiment against the proceedings have sent the approval ratings of Prime Minister Fumio Kishida to record lows, around 29%, according to a poll conducted by one of Japan’s major newspapers, Mainichi Shimbun. In response, Kishida has apologized and asked members of his party to cut ties with the Unification Church.
Japanese officials have also sought to placate the public anger ahead of the funeral.
Another public opinion poll conducted by Mainichi found around 62 % of respondents did not think a state funeral was appropriate for Abe, citing the high expenses and that he was not worthy of the honor, Reuters reported.
The assassination of Japan's most prominent politician shook a nation that has one of the strictest gun laws in the world.
The suspect, Tetsuya Yamagami, a 41-year-old unemployed man who shot Abe in close range twice with a homemade firearm, told police he wanted to kill the former leader because of his links to the Unification Church, which he said left his mother bankrupt, officers told reporters shortly after his arrest.
The church has confirmed Yamagami's mother was a member of its congregation.
Abe pursued a strong nationalistic agenda during his tenure as the leader of Japan, including attempts to revise the country's constitution to broaden limits on its military that only allows it to act in self-defense.