The two unnamed individuals say they are sexually attracted to animals.
They sought to get the court in Karlsruhe to consider whether the existing rules are unconstitutional.
But the court threw out their claim, ruling that the effect of the ban on the complainants' right to sexual self-determination was justified.
The court said that protecting animal welfare by seeking to prevent them being the victim of sexual assaults was a legitimate aim of the law -  which remains unchanged after the court's decision.
Germany's animal protection laws set out fines of up to â‚¬25,000 ($27,700; Â£19,000) for forcing animals to participate in what is termed as unnatural behaviour.
Two complainants have failed in their attempt to get Germany's constitutional court to consider their claim against the laws banning sex with animals.