He described feeling "drunk" after the second dose and said when he came to his pants were removed and had been folded and placed on a chair.
It was at this point that The Doctors practice nurse Anna McKinley said she distinctly heard the male cry out "Why are you touching my balls?"
She said she was stunned and immediately pulled the curtain back to see what was going on.
"I noticed a stunned look on Dr Lim's face. It's like I can equate it to a child being caught with his hand in a cookie jar.
"I just couldn't believe that this was happening to him, that he was being touched by the doctor that was meant to be there to look after him."
The male said he was then moved by Lim to an enclosed, darkened room to "sleep".
"I can remember lying on the bed and while I was lying there I felt his hand go down my pants."
He described feeling "disgusted" and said although it felt like a dream he was was "100 per cent" sure Lim had handled his private parts.
"I didn't think I should [tell anyone]. I thought it was a dream really. I thought about it all the next day."
The man said he didn't expect a doctor to do that, stating "Everyone trusts a doctor."
In his opening address yesterday Lim's defence counsel Harry Waalkens QC said Lim "categorically denies" the allegations and that Lim being "overtly gay" created a situation "ripe for misunderstanding".
"We anticipate that it's likely each of these four young men recognised that when they came into the consultation they knew that he was demonstrably, overtly as I say, a gay person."
The court heard from emergency medicine expert Dr Craig Ellis yesterday who testified Midazolam was "used extensively" in the emergency department at Hawke's Bay Hospital and was given to patients to alleviate their anxiety and give them a "form of amnesia".
Dr Ellis said while hallucinations did occur, he had administered the drug hundreds of time and never knowlingly had a patient suffer hallucinations of a sexual nature.
The trial is set to continue into next week.