Eight people were injured, one seriously, by the attacker who struck in the Harajuku fashion district shortly after midnight. The shrine is a popular New Year's Eve destination.
Police took into custody a man in his 20s and said he is suspected of intentionally trying to kill people by driving the vehicle through the street.
The 21-year-old suspect, Kazuhiro Kusakabe, was arrested and questioned, Tokyo Metropolitan police.
At least eight people were injured when a man deliberately drove his auto into a crowded Tokyo street filled with people who had gathered for the city's New Year's festivities.
"It was not immediately clear whether he was referring to a specific execution or Japan's system of capital punishment", the news agency reported. There was a tank of kerosene in the rental auto, which he said he planned to use to burn the vehicle, the investigative sources said. "Really scary, isn't it?" one bystander told NHK. As I walked closer toward the scene, many more people had fallen on the ground.
Police took into custody a man in his 20s but did not further identify him.
A man was filmed shouting "Allahu Akbar" as he was bundled into a police van, the Evening Standard reported.
Eight people were hit by the vehicle, including a teenage boy who is in critical condition, the police said.
"I heard the man say, As long as you keep bombing these countries this is going to keep happening", the producer, Sam Clack, told BBC 5 Live radio.
The blast, which destroyed 35 units, killed at least seven people and left hundreds homeless in freezing temperatures.