But the court ruled they had not given enough specific reasons to justify the measures applied.
Mr Gbagbo was arrested in April after he refused to accept the results of a November 2010 poll. His refusal to cede power sparked a four-month conflict.
An estimated 3,000 people were killed in the outbreak of violence.
The General Court, an independent court attached to the European Court of Justice, ruled that EU member states "did not provide a sufficient statement of reasons as to how Nadiany Bamba obstructs the process of peace and reconciliation in Ivory Coast".
Mr Gbagbo's second wife is listed as director of the Cyclone group, which publishes the newspaper Le Temps.
EU states said that she had blocked peace and reconciliation processes through "public incitement to hatred and violence and through participation in disinformation campaigns", the court said.
But, after an accelerated hearing by five judges, the court ruled that the reasons for the asset freeze had not been sufficiently detailed, specific, or communicated properly to Ms Bamba.
The restrictions against Mr Gbagbo's second wife are to be lifted following the judgement, pending appeal.
In May, authorities in Switzerland said they had frozen assets worth 70m Swiss francs (£49m; $81m) linked to the former president.
The country's President Alassane Ouattara, officially inaugurated in May, has urged the EU to lift sanctions imposed, for example, on the ports of Abidjan and San Pedro in a bid to restart the ailing economy.