Acting Judge Chris Eksteen did not give the reasons for his ruling in the High Court in Pretoria.
However, he said that, in the light of the legal position and the evidence presented to court, he could not grant a discharge at this stage.
The State on Tuesday conceded that it had not proved the first charge against Els, namely that he indecently assaulted Klay while he was under the age of 12.
Els has pleaded not guilty to that charge and to charges of indecently assaulting Klay while he was between the ages of 12 and 16 and soliciting Klay to commit indecent acts while he was under the age of 16.
Eksteen told Els's advocate Danie Dorfling that the judgment might come as a "surprise and a shock" and postponed the trial until Wednesday to give Els time to consider his legal position.
Dorfling earlier argued that Klay's evidence about the alleged sexual abuse was such a "confusing mess" and so unreliable that no reasonable court could convict him.
He said the court should not be influenced by newspaper reports, rumours, suspicion, public opinion or the adage that "where there was smoke there was fire".
Prosecutor Corlie Bouwer stressed that abused children should have a right of recourse.
They should not be penalised for only revealing their alleged abuse years later, as was often the case with such incidents which usually took place behind closed doors.
She said the burning question was why Klay would put his reputation and career on the line and testify in brutal and humiliating detail about his alleged homosexual deeds with Els in an open court in front of a merciless media.
"... There's no explanation from Els why Klay would come and stand here for eight days and drag his soul through hell," she said.
Bouwer said all the court had to decide at this stage was if there was enough evidence on record to establish a case that Els had to answer.
She stressed the psychologist's findings that Klay showed typical symptoms of an adult survivor of childhood sexual abuse.
"The accused admitted that he had an especially long and close relationship with Klay.
"If he did not do it, who did? Who would be better than Els to tell the court who else could have had such an influence of Klay's life?"
The trial continues on Wednesday. It is not yet known if Els will testify in his defence.
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