The rationale in this case was that the exclusionary rule was meant to deter the police from acting improperly. It was not meant to try to compensate defendants for invasion of their privacy or to punish judges for making mistakes.
In this case, the police were investigating a suspected drug ring. A judge gave them a search warrant based on surveillance that they had done. When they served the search warrant, they found a large quantity of drugs. So, the police, acting on a search warrant, found drugs and charged Leon with a crime.
The problem was that the search warrant which the police had obtained was later ruled to have been invalid. A court ruled that the judge who issued the warrant had made a mistake and the warrant should not have been issued. What the Supreme Court ruled was that this was a mistake on the part of the judge, not on the part of the police. Since the exclusionary rule, they held, was meant to prevent the police from acting wrongly, it should not be used to punish the police when they had acted in good faith, thinking they had a proper warrant.