The murder of Japan's best-known politician rattled the country and sent shockwaves around the world, particularly given the nation's low levels of violent crime and strict gun laws.
AFP journalists saw the vehicle enter Abe's residence in the capital, while senior members of his ruling Liberal Democratic Party, dressed in black, lined up to pay their respects.
The man accused of Friday's shooting is in custody, with police saying he had confessed to killing the former premier, motivated by a belief Abe was linked to an unspecified organisation.
Police were investigating the unemployed 41-year-old's background, including claims he had served in Japan's navy, and said he appeared to have used a handmade gun.
Abe was delivering a speech in Nara ahead of Sunday's upper house elections when he was shot, and campaigning resumed Saturday with politicians saying they were determined to show democracy would prevail.
"We absolutely must not tolerate violence during an election to suppress speech," Prime Minister Fumio Kishida told around 600 supporters in central Japan's Yamanashi region, according to the Yomiuri Shimbun newspaper.
The Yomiuri and other Japanese media at Kishida's first campaign event since the assassination described a tense mood and high levels of security, with a metal fence put up to separate the leader from the crowd.
Doctors said Friday that Abe showed no vital signs when he arrived and died of enormous blood loss, despite massive transfusions.
They described multiple wounds to the politician's neck, with the internal damage reaching as deep as his heart.
Abe's murder shook Japan, with Kishida describing the killing as a "barbaric act" that was "unforgivable".
Kishida was visibly emotional after the former leader's death was confirmed, saying he was "lost for words", and is expected to visit Abe's Tokyo residence on Saturday to pay his respects.
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