The outbreak is the first in 70 years in Japan and has so far infected 55 people, including a young model who has posed for Japanese Playboy and had been sent to the park for a photo shoot.
The disease, also called "tropical 'flu", is spread by the tiger mosquito, a species endemic to Japan.
No one has so far died in Japan from the disease, which claims scores of lives every year in other, more infected parts of the world.
But Japanese health officials, along with the public at large, tend to be cautious.
Last week teams sprayed pesticide in the park to try to kill off the insect colony.
They then set traps to catch the creatures and test them. Four of the 10 sites targeted found mosquitoes that were carrying the disease, indicating a large area was affected.
"After detecting dengue virus from a wide area of Yoyogi Park, the Tokyo government in order to ensure public safety is to close the area from 2 pm today for the time being," the metropolitan government said in a statement.
Dengue fever was stamped out in Japan at the end of World War II, even though its mosquito host remains endemic.