The election rerun will not change the result, as Antonio Costa's Socialist Party secured a landslide victory.
Portugal's new Socialist government may not be sworn-in until March due to thousands of invalid election votes.
On Tuesday, the country's Constitutional Court voided around 80% of mail-in ballots that were cast by Portuguese citizens living abroad in Europe.
The court said that more than 157,000 votes were unaccompanied by an identity document and were therefore invalid.
The election must now be rerun at 139 voting stations across Europe, it added.
Portuguese political parties had earlier reached a verbal agreement to scrap the requirement for voters to send a copy of an official ID document with their postal ballots.
But the 13 judges at Portugal’s highest court said that decision was “grossly illegal” because it contravened electoral law.
The court's decision has not just embarrassed politicians but has also delayed Portugal's 2022 state budget until June.
But a rerun of balloting will not affect the final result, as the Socialist party of incoming Prime Minister António Costa collected a landslide of 119 seats in the 230-seat parliament.
Costa -- who had expected to take office next week -- apologised to voters and said the issue should “serve as a lesson” for politicians to write better laws.
"There is a decision by the Constitutional Court that must be respected," Costa said on Tuesday evening.
A second election vote for Portuguese citizens abroad in Europe is due to take place on 27 February.