"I maintain I am innocent of the alleged offences and will plead not guilty to the charges," Selebi said in an affidavit read to the court.
He appeared relaxed during the hearing, and smiled at family and friends.
Selebi was suspended from his job as police commissioner and resigned the largely ceremonial post as president of the international police organisation Interpol, after the National Prosecuting Authority last month announced the upcoming charges against him.
Prosecutors allege Agliotti gave Selebi cash handouts "as and when he requested," bought clothes for him and his family and gave him $4,400 to pay for a dinner in Paris when he was elected head of Interpol in 2004.
The payments totalled at least $175,000 between 2000 and 2005, the prosecuting authority said.
Selebi has also been accused of turning a blind eye to Agliotti's involvement in transporting large quantities of illegal drugs.
The prosecutors said Selebi also informed Agliotti that British intelligence authorities were investigating him.
In a plea bargain last year, Agliotti admitted to smuggling drugs into the country and received a suspended 10-year prison sentence and a fine. In return, he agreed to testify against drug gangs. Prosecutors have refused to confirm media reports that Agliotti may be the star witness in a trial against Selebi.
Meanwhile Thabo Mbeki, South Africa's president, placed Selebi on "extended leave" in January, but has resisted pressure to sack the police chief.
Mbeki suspended Vusi Pikoli, the chief prosecutor, in September after he issued a warrant for the Selebi's arrest.
Mokotedi Mpshe, the acting prosecuting chief, withdrew the warrant and ordered an independent investigation of the case.