Reg Traviss, who was dating Winehouse at the time of her death from alcohol poisoning in July 2011, is accused of sexually assaulting the woman at his Marylebone flat after a night of drinking on December 30 last year.
Prosecutor Katherine Lumsdon opened the case in Southwark Crown Court by saying that the defendant twice awoke to find Traviss having sex with her, and on one occasion told her: "I always wanted to do this to you."
Lumsdon stated: "She said she would not have consented to sex even if she had been conscious.
"She asked Reg to put her in a cab so that she could go home. He suggested she stay at his as it was closer. She was also aware that a black cab was unlikely to take her as she couldn't stand.
"She remembers him asking, 'Would you like to stay at mine?' She does not remember her reply, but assumes she said yes. That's the last thing she remembers before waking up in his bed because of an acute pain."
The prosecutor says Traviss stopped the first time the woman awoke, offered her more alcohol and continued "acting as if nothing had happened at all".
The woman claims to have gone back to sleep and awoke to find Traviss having sex with her again, but "felt so tired and so weak that she passed out", the Daily Mail reports.
The court heard that the next day "she asked him where her knickers were and he said, 'I actually want to keep them', and she didn't press the matter as she just wanted to get home".
The complainant said that she could not "understand how somebody so nice and gentlemanly could do something like that", adding that Traviss had been "shattered and quite distressed" since Winehouse's death five months prior.
Traviss was arrested on April 5. The woman had been reluctant to report the alleged incident due to his status and, according to the prosecution, "thought it would be easier to forget about it".
Traviss claims that upon returning to his home, the woman lit candles and told him not to sleep on the sofa, but join her in the bed, where they had consensual sex.
He says they were equally as drunk and parted the next day with a "big cuddle and a kiss".
Traviss denies two counts of rape. The trial continues.