The case centered on whether German authorities were breaching protocol when they convicted Brueckner last year for the rape of a 72-year-old woman in 2005.
Brueckner challenged the rape sentencing in Germany on the grounds that the charge was not cited on the original 2018 arrest warrant.
His lawyer, Friedrich Fulscher, challenged the validity of the warrant, arguing for a breach of international protocol in trialing him on a separate charge.
The ruling found the conviction of rape and extortion was justified and Italian authorities who handed Brueckner to Germany had given their consent for him to also be additionally prosecuted for the rape.
The 43-year-old is currently serving a 21-month sentence for drug trafficking in the German city of Kiel.
If the separate case had been thrown out by the court, Brueckner would have been released when his current sentence is due to end on 7 January 2021.
The ECJ ruling now means when the jail term for drug trafficking ends, the seven-year prison time for the rape will begin.
In June, German prosecutors, led by Hans Christian Wolters, announced they had identified the convicted paedophile and rapist Brueckner as the prime suspect in the McCann investigation.
The British three-year-old disappeared from a holiday apartment in 2007 in the resort of Praia Da Luz, Portugal, while her parents dined with friends nearby.
Despite an international investigation and ongoing manhunt, no traces of McCann have been found and no convictions have been made.
On Tuesday, Mr Wolters announced there is “material evidence” that McCann is dead.
The 43-year-old had been living nearby the resort at the time and telephone data suggests he was near the apartment just hours before she was last seen.
Authorities say they do not yet have enough evidence to hold him in prison for McCann's disappearance.
Brueckner denies having anything to do with McCann while his lawyer, Fulscher, told The Sun on Monday he had proof that Brueckner was innocent and that German authorities had the wrong man.
Meanwhile, British police are still treating the case as a missing person’s inquiry.