Babalele is being prosecuted by the Economic and Financial Crimes Commission for allegedly laundering $140,000 in the build-up to the last general elections.
Atiku contested and lost to President Muhammadu Buhari in the election.
Babalele was first arraigned on August 14, 2019 before Justice Nicholas Oweibo.
Following the re-assignment and transfer of the case file to Justice C.J. Aneke, the defendant was re-arraigned on Tuesday.
He pleaded not guilty to the charges.
Justice Aneke granted his request to continue on the N20m bail with one surety earlier granted him in August by Justice Oweibo.
After his re-arraignment, Babalele applied to the court for the release of his passport to enable him travel abroad for medical treatment.
But the prosecuting counsel for the EFCC, Rotimi Oyedepo, opposed the application, arguing that there was no proof that Babalele’s condition could not be treated in Nigeria.
Justice Aneke adjourned till October 11 for ruling.
In the charges, the EFCC accused Babalele of asking Bashir Mohammed to make a cash payment of $140,000 without going through any financial institution.
The EFCC lawyer, Oyedepo, said the money exceeded the threshold stipulated by the money laundering law.
He said Babalele made the transaction on February 20, 2019, three days to the presidential election, in contravention of Section 18 (c) of the Money Laundering (Prohibition) Act, 2011 and was liable to be punished under Section 16(2)(b) of the same Act.
But the defendant denied the allegations.