The decision followed 16 rulings from lower courts, with one saying the gap was unconstitutional and eight calling it in a state of unconstitutionality.
With Foreign Minister Yoshimasa Hayashi having been selected for the new No. 3 district, Prime Minister Fumio Kishida's caucus has come out on top over the Abe faction.
Among the 15 justices of the top court's Grand Bench, 14 ruled the 2021 Lower House election was constitutional, while one said it was unconstitutional.
The revised law, which will remove one seat each from 10 prefectures and distribute 10 to five other prefectures, will be put into effect a month after its promulgation.